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diff --git a/_book/develop-path1.html b/_book/develop-path1.html
index 1de92b86..d41c1be3 100644
--- a/_book/develop-path1.html
+++ b/_book/develop-path1.html
@@ -1112,8 +1112,8 @@ <
Input_Conv::Convert()
这个函数实现了从 Input 类对象的数据成员到 GlobalV 和 GlobalC 等全局变量集合的转换。相当于从 Input 到 GlobalV 和 GlobalC，以及其他直接的类的参数上载：
-其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
+其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
void Input_Conv::Convert(void)
{
....
@@ -1308,7 +1308,7 @@
不要忘记我们已经完成 Driver::reading() 函数内容，到达 Driver::atomic_world()。这一点从本文档设置的分级目录中也可以看得到。
-cppvoid Driver::init()
+void Driver::init()
{
this->reading();
this->atomic_world(); // <- here!
@@ -1518,7 +1518,7 @@ 从 SIAB 到 ABACUS（一）：准备工作（施工中 🚧）
下篇：Introduction to ABACUS: Path to PW calculation - Part 2
@@ -1562,7 +1562,7 @@ No results matching "
var gitbook = gitbook || [];
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V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","attributes":{},"skip":false,"key":"1.1.15.5"},{"backlink":"abacus-surface6.html#fig1.1.16.1","level":"1.1.16","list_caption":"Figure: 一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","alt":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","nro":14,"url":"picture/fig_surface6-1.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","attributes":{},"skip":false,"key":"1.1.16.1"},{"backlink":"abacus-surface6.html#fig1.1.16.2","level":"1.1.16","list_caption":"Figure: 静电势（Electrostatic Potential）沿超胞Z轴变化图","alt":"静电势（Electrostatic Potential）沿超胞Z轴变化图","nro":15,"url":"picture/fig_surface6-2.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"静电势（Electrostatic Potential）沿超胞Z轴变化图","attributes":{},"skip":false,"key":"1.1.16.2"},{"backlink":"develop-path4.html#fig1.2.9.1","level":"1.2.9","list_caption":"Figure: ","alt":" 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1)","alt":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","nro":21,"url":"picture/fig_path5-11.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","attributes":{},"skip":false,"key":"1.2.10.3"},{"backlink":"develop-path5.html#fig1.2.10.4","level":"1.2.10","list_caption":"Figure: 1-dimensional example","alt":"1-dimensional example","nro":22,"url":"picture/fig_path5-12.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"1-dimensional example","attributes":{},"skip":false,"key":"1.2.10.4"},{"backlink":"develop-path5.html#fig1.2.10.5","level":"1.2.10","list_caption":"Figure: 2-dimensional example","alt":"2-dimensional example","nro":23,"url":"picture/fig_path5-13.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"2-dimensional example","attributes":{},"skip":false,"key":"1.2.10.5"}]},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"develop-path1.md","mtime":"2023-10-04T14:18:52.079Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-10-04T15:29:41.868Z"},"basePath":".","book":{"language":""}});
});
diff --git a/_book/develop-path2.html b/_book/develop-path2.html
index 191dfe74..d829579b 100644
--- a/_book/develop-path2.html
+++ b/_book/develop-path2.html
@@ -1028,7 +1028,7 @@ // a(i) is lattice vector
}
-我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
+我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
UnitCell::read_atom_positions()
🔧重构思考
@@ -1042,7 +1042,7 @@
::
GlobalFunc::READ_VALUE( ifpos, Coordinate);
STRU 第二行指定坐标类型，被读取为 UnitCell::Coordinate。UnitCell::Coordinate 在 STRU 里有不同选项，⚙ 决定原子的具体位置和单位：
-if(Coordinate != "Cartesian"
+ if(Coordinate != "Cartesian"
&& Coordinate != "Direct"
&& Coordinate != "Cartesian_angstrom"
&& Coordinate != "Cartesian_au"
@@ -1092,7 +1092,7 @@ int na = 0;
+ int na = 0;
this->nat = 0;
assert(ntype>0);
for (int it = 0;it < ntype; it++)
@@ -1105,7 +1105,7 @@ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
bool sequence_match = false;
for(int it2=0; it2<ntype; it2++)
{
@@ -1121,7 +1121,7 @@ }
读取当前原子类型的 starting_magnetization、原子总数 na
-ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
...
ModuleBase::GlobalFunc::READ_VALUE(ifpos, na);
this->atoms[it].na = na;
@@ -1149,17 +1149,17 @@ [
it].m_loc_ = new ModuleBase::Vector3<double>[na];
⚙ 然后在 ATOMIC_POSITIONS 中读取：
-atoms[it].mass = this->atom_mass[it];
+ atoms[it].mass = this->atom_mass[it];
❗ 此处的 atoms[it].mass 与 this->atom_mass[it] 的用法与 atomis[it].label 与 this->atom_label[it] 不同：传值 vs 核对。
接下来读取类中每个原子的速度信息，在做分子动力学模拟的时候可能需要用到：
-for (int ia = 0;ia < na; ia++)
+ for (int ia = 0;ia < na; ia++)
{
ifpos >> v.x >> v.y >> v.z;
然而，当前 STRU 文件在 ATOMIC_POSITIONS 的设计比较复杂，其可以包括任何一组 atom-specific 数据，且数量和顺序均不受限制，这导致判断条件变得复杂，详见 module_cell/read_atoms.cpp:line 536 - 567（link）。
atoms[it].mag 的赋值并非直接读取：
-else if ( tmpid == "mag" || tmpid == "magmom")
+ else if ( tmpid == "mag" || tmpid == "magmom")
{
set_element_mag_zero = true;
double tmpamg=0; ifpos >> tmpamg;
@@ -1185,7 +1185,7 @@ }
⚙ 若 mag/magmom 后有一个值，则读取其值赋给 atoms[it]::mag[ia]，将 input_vec_mag 置为 false，若有三个值，则三个值依次被传入 atoms[it].m_loc_[ia].x, atoms[it].m_loc_[ia].y 和 atoms[it].m_loc_[ia].z，并将 input_vec_mag 置为 true，之后其向量模长为 atoms[it]::mag[ia]，然后在使用 angle1, angle2 来重新生成 mag。
-if(GlobalV::NSPIN==4)
+ if(GlobalV::NSPIN==4)
{
if(GlobalV::NONCOLIN)
{
@@ -1227,7 +1227,7 @@ pw.x input description
ABACUS 对 nspin=4 情况的参数处理：
//module_io/input_conv.cpp line 376
if (INPUT.noncolin || INPUT.lspinorb)
@@ -1312,7 +1312,7 @@
UnitCell::setup_cell(): the rest, and an example of backtracking unclear variable
离开 STRU 文件的解析部分，接下来计算了初始磁化强度：
-//after read STRU, calculate initial total magnetization when NSPIN=2
+ //after read STRU, calculate initial total magnetization when NSPIN=2
if(GlobalV::NSPIN == 2 && !GlobalV::TWO_EFERMI)
{
for(int it = 0;it<this->ntype; it++)
@@ -1326,31 +1326,25 @@ if (std::abs(INPUT.nupdown) > 1e-6)
- {
- GlobalV::TWO_EFERMI = true;
- GlobalV::nupdown = INPUT.nupdown;
- }
-
-因此 GlobalV::TWO_EFERMI 变量实际依赖于 INPUT.nupdown。
-
-- 接下来在
module_io/input.cpp 中寻找含 INPUT.nupdown 的 if(strcmp(...)) 单元，查看在 INPUT 文件中是何参数赋予其具体值：
-
-else if (strcmp("nupdown", word) == 0)
+在 module_io/input_conv.cpp 中寻找该变量，是何变量赋其值，发现： if (std::abs(INPUT.nupdown) > 1e-6)
{
- read_value(ifs, nupdown);
- }
+ GlobalV::TWO_EFERMI = true;
+ GlobalV::nupdown = INPUT.nupdown;
+ }
-即 INPUT.nupdown 在 INPUT 中也为 nupdown。接下来打开 Full keyword list 寻找其解释。
-
+ 因此 GlobalV::TWO_EFERMI 变量实际依赖于 INPUT.nupdown。
+接下来在 module_io/input.cpp 中寻找含 INPUT.nupdown 的 if(strcmp(...)) 单元，查看在 INPUT 文件中是何参数赋予其具体值： else if (strcmp("nupdown", word) == 0)
+ {
+ read_value(ifs, nupdown);
+ }
+
+即 INPUT.nupdown 在 INPUT 中也为 nupdown。接下来打开 Full keyword list 寻找其解释。
得到结果，即 nupdown 为 spin up 和 spin down 电子数量差值：
因此该部分逻辑为：若未使用 nupdown 来指定单电子数量，则对每种原子内每个原子，累加其 mag/magmom，即磁矩模长，赋予 GlobalV::nupdown。❗ 但对于两种方式均赋予，但值不一致的情况未进行处理。
接下来根据在 STRU 中读取的晶胞参数，计算晶胞体积，并计算倒空间矢量（在上篇中已经对 latvec, G, GT, GGT 有所介绍，invGGT 的意义也不言自明）：
-this->omega = std::abs( latvec.Det() ) * this->lat0 * lat0 * lat0 ;
+ this->omega = std::abs( latvec.Det() ) * this->lat0 * lat0 * lat0 ;
this->GT = latvec.Inverse();
this->G = GT.Transpose();
@@ -1442,7 +1436,7 @@ =
static_cast<ModulePW::PW_Basis_Big*>(pw_rho);
对于 ESolver 本身，其指针对象 p_esolver 实际上也有类似操作：
-//Some API to operate E_Solver
+ //Some API to operate E_Solver
void init_esolver(ESolver*& p_esolver)
{
//determine type of esolver based on INPUT information
@@ -1907,7 +1901,7 @@ Introduction to ABACUS: Path to PW calculation - Part 1
下篇：Introduction to ABACUS: Path to PW calculation - Part 3
@@ -1951,7 +1945,7 @@ No results matching "
var gitbook = gitbook || [];
gitbook.push(function() {
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采用PBE交换关联泛函和自旋极化得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出不加电场时，两个自旋方向的能带图几乎一样，都有带隙。","alt":"采用PBE交换关联泛函和自旋极化得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出不加电场时，两个自旋方向的能带图几乎一样，都有带隙。","nro":12,"url":"picture/fig_surface5-4.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"采用PBE交换关联泛函和自旋极化得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出不加电场时，两个自旋方向的能带图几乎一样，都有带隙。","attributes":{},"skip":false,"key":"1.1.15.4"},{"backlink":"abacus-surface5.html#fig1.1.15.5","level":"1.1.15","list_caption":"Figure: 采用PBE交换关联泛函和自旋极化，再给体系加上0.1 V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","alt":"采用PBE交换关联泛函和自旋极化，再给体系加上0.1 V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","nro":13,"url":"picture/fig_surface5-5.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"采用PBE交换关联泛函和自旋极化，再给体系加上0.1 V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","attributes":{},"skip":false,"key":"1.1.15.5"},{"backlink":"abacus-surface6.html#fig1.1.16.1","level":"1.1.16","list_caption":"Figure: 一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","alt":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","nro":14,"url":"picture/fig_surface6-1.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","attributes":{},"skip":false,"key":"1.1.16.1"},{"backlink":"abacus-surface6.html#fig1.1.16.2","level":"1.1.16","list_caption":"Figure: 静电势（Electrostatic Potential）沿超胞Z轴变化图","alt":"静电势（Electrostatic Potential）沿超胞Z轴变化图","nro":15,"url":"picture/fig_surface6-2.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"静电势（Electrostatic Potential）沿超胞Z轴变化图","attributes":{},"skip":false,"key":"1.1.16.2"},{"backlink":"develop-path4.html#fig1.2.9.1","level":"1.2.9","list_caption":"Figure: ","alt":" ","nro":16,"url":"picture/fig_path4-1.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":" ","attributes":{},"skip":false,"key":"1.2.9.1"},{"backlink":"develop-path4.html#fig1.2.9.2","level":"1.2.9","list_caption":"Figure: PW_Basis::distribute_r()：设一个pool中有5个processors","alt":"PW_Basis::distribute_r()：设一个pool中有5个processors","nro":17,"url":"picture/fig_path4-2.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"PW_Basis::distribute_r()：设一个pool中有5个processors","attributes":{},"skip":false,"key":"1.2.9.2"},{"backlink":"develop-path4.html#fig1.2.9.3","level":"1.2.9","list_caption":"Figure: this->count_pw_st(st_length2D, st_bottom2D)","alt":"this->count_pw_st(st_length2D, st_bottom2D)","nro":18,"url":"picture/fig_path4-3.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"this->count_pw_st(st_length2D, st_bottom2D)","attributes":{},"skip":false,"key":"1.2.9.3"},{"backlink":"develop-path5.html#fig1.2.10.1","level":"1.2.10","list_caption":"Figure: 善用Ctrl+F","alt":"善用Ctrl+F","nro":19,"url":"picture/fig_path5-9.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"善用Ctrl+F","attributes":{},"skip":false,"key":"1.2.10.1"},{"backlink":"develop-path5.html#fig1.2.10.2","level":"1.2.10","list_caption":"Figure: klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","alt":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","nro":20,"url":"picture/fig_path5-10.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","attributes":{},"skip":false,"key":"1.2.10.2"},{"backlink":"develop-path5.html#fig1.2.10.3","level":"1.2.10","list_caption":"Figure: klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","alt":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","nro":21,"url":"picture/fig_path5-11.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","attributes":{},"skip":false,"key":"1.2.10.3"},{"backlink":"develop-path5.html#fig1.2.10.4","level":"1.2.10","list_caption":"Figure: 1-dimensional example","alt":"1-dimensional example","nro":22,"url":"picture/fig_path5-12.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"1-dimensional example","attributes":{},"skip":false,"key":"1.2.10.4"},{"backlink":"develop-path5.html#fig1.2.10.5","level":"1.2.10","list_caption":"Figure: 2-dimensional example","alt":"2-dimensional example","nro":23,"url":"picture/fig_path5-13.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"2-dimensional example","attributes":{},"skip":false,"key":"1.2.10.5"}]},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"develop-path2.md","mtime":"2023-10-04T14:37:12.149Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-10-04T15:29:41.868Z"},"basePath":".","book":{"language":""}});
});
diff --git a/_book/develop-path3.html b/_book/develop-path3.html
index b8de33d9..09176394 100644
--- a/_book/develop-path3.html
+++ b/_book/develop-path3.html
@@ -750,11 +750,11 @@ Driver
-Driver::atomic_world()
-Driver::driver_run()
-多层继承：Init() functions in esolver class
-Trigger: ESolver_FP::Init()
+Driver
+Driver::atomic_world()
+Driver::driver_run()
+多层继承：Init() functions in esolver class
+Trigger: ESolver_FP::Init()
承接上篇中已经导入的结构信息，以及了解到构造函数及其伴随的变量初始化和 ABACUS 里应用到的 C++ 多态编程，接下来即将（逐渐）步入 ABACUS 的核心内容。我们暂时跳过位于 source/driver_run.cpp:driver_run() 的：
// 3. For these two types of calculations
// nothing else need to be initialized
@@ -830,14 +830,14 @@ }
同理，ESolver_KS 的数据成员，也被 ESolver_KS_PW 继承。ESolver_FP::Init() 首先调用 UnitCell::read_pseudo() 函数进行赝势文件读取，而将赝势文件读取任务放在 FP 层级下，也暗示对于 ABACUS 的第一性原理方法实现来讲，都需要使用赝势。
-Pseudopotential import: UnitCell::read_pseudo()
+Pseudopotential import: UnitCell::read_pseudo()
void UnitCell::read_pseudo(std::ofstream &ofs)
{
read_cell_pseudopots(GlobalV::global_pseudo_dir, ofs);
在解读赝势文件读取功能之前，首先需要对赝势文件的结构和信息做一定程度的了解。
-# ONCV pseudopotential file
-## Section 0: Norm-conserving conditions, generation of pseudopotential and header of exact UPF file
+ONCV pseudopotential file
+Section 0: Norm-conserving conditions, generation of pseudopotential and header of exact UPF file
赝势的意义不言自明，其中模守恒赝势需满足如下条件：
- （赝势得到的能级和全电子方法求解的能级一样，这里 ps 代表 pseudopotentials）
@@ -852,7 +852,7 @@ V_l(r)=\frac{1}{\phi^\text{ps}_l(r)}[\epsilon^\text{ps}_l-\frac{\hbar^2}{2m}\frac{l(l+1)}{r^2}+\frac{\hbar^2}{2m}\frac{d^2}{dr^2}]\phi^\text{ps}_l(r)，解得。
- 扣除中 Hartree、xc 部分，得到：。
-更多细节见
+更多细节见：www.tcm.phy.cam.ac.uk
<UPF version="2.0.1">
<PP_INFO>
<!-- omitted information here -->
@@ -865,8 +865,8 @@ <!-- -->
从 UPF 文件（注意 UPF 文件也有不同的版本，目前 ABACUS 都支持，若有不支持的，可以提 Github 的 issues 进行讨论）开始，截止到 <PP_HEADER> 之前，提供了赝势文件的作者信息，引用信息以及生成赝势文件所使用的程序和相应输入文件，并附带输入文件参数中的解释。由于此块内容对实际计算并不起作用，因此暂时略过。
-## Section 1:
-<PP_HEADER
+Section 1:
+ <PP_HEADER
generated="Generated using ONCVPSP code by D. R. Hamann" author="Martin Schlipf and Francois Gygi"
date="150105" comment=""
element="Al"
@@ -890,8 +890,8 @@ number_of_proj
="4"/>
<PP_HEADER> 部分尽管已经位于所谓“not human readable”区域，但也并非如此。这部分“标签”（HTML 语境）/block 实际上包含了众多精简过的信息，如元素名称（element）、赝势类型（pseudo_type，模守恒，norm-conserving，NC），相对论效应（relativistic），是否为超软赝势等等信息。当前 Al 理论上其原子序数 13，因此有 13 个电子，但此处 z_valence 参数为 11，即有两个 1s 电子被赝化，只留下 2s, 2p, 3s, 3p 电子共 2+6+2+1 个。对于某些元素，甚至有大核赝势与小核赝势之分，根据赝化电子数量不同进行区分。显而易见地，赝化电子数量越多，则计算量越小，但计算结果的精确程度可能更低。
-## Section 2:
-<PP_MESH>
+Section 2:
+ <PP_MESH>
<PP_R type="real" size=" 602" columns="8">
0.0000 0.0100 0.0200 0.0300 0.0400 0.0500 0.0600 0.0700
<!-- omitted information here -->
@@ -907,8 +907,8 @@ </PP_MESH>
这部分开始出现了关于实空间格点相关量的定义。在 tag 中不仅指定数据类型为实数，也指定当前数据的长度（size），以及数据存储的列数（columns = 8）。PP_R 为格点坐标，PP_RAB 则为格点间距。
-## Section 3:
-<PP_LOCAL type="real" size=" 602" columns="4">
+Section 3:
+ <PP_LOCAL type="real" size=" 602" columns="4">
-4.5793174225E+01 -4.5788454271E+01 -4.5774276797E+01 -4.5750659428E+01
<!-- omitted information here -->
-3.6912752197E+00 -3.6850921941E+00 -3.6789298138E+00 -3.6727880140E+00
@@ -917,8 +917,8 @@ <PP_LOCAL>
部分开始，正式开始写入赝势的具体数值，建立在 <PP_R> 和 <PP_RAB> 所描述的实空间格点上。。<PP_LOCAL> 正是赝势的局域势部分。
-## Section 4:
-<PP_NONLOCAL>
+Section 4:
+ <PP_NONLOCAL>
<PP_BETA.1
type="real"
size=" 602"
@@ -938,8 +938,8 @@ cutoff_radius_index
=" 246" cutoff_radius=" 2.4500000000E+00" >
<!-- omitted information here -->
</PP_BETA.2>
- <PP_BETA.3 type="real" size=" 602" columns="4" index="3" angular_momentum="1"<strong>
-</strong> cutoff_radius_index=" 246" cutoff_radius=" 2.4500000000E+00" >
+ <PP_BETA.3 type="real" size=" 602" columns="4" index="3" angular_momentum="1"
+ cutoff_radius_index=" 246" cutoff_radius=" 2.4500000000E+00" >
<!-- omitted information here -->
</PP_BETA.3>
<PP_BETA.4 type="real" size=" 602" columns="4" index="4" angular_momentum="1"
@@ -956,7 +956,7 @@ \hat{V}^\text{NL}=\sum_{ij}{|\beta_i\rangle D_{ij}\langle\beta_j|}。其中一般被称为非局域势投影子（projector）。
-## Section 5: and
+Section 5: and
<PP_PSWFC>
</PP_PSWFC>
<PP_RHOATOM type="real" size=" 602" columns="4">
@@ -975,7 +975,7 @@ |\beta\rangle和 pswfc 已经乘径向坐标。
-# UnitCell::read_cell_pseudopots()
+UnitCell::read_cell_pseudopots()
link to Github -> link
void UnitCell::read_cell_pseudopots(const std::string &pp_dir, std::ofstream &log)
{
@@ -1030,7 +1030,7 @@ while (ifs.good())
+ while (ifs.good())
{
ifs >> dummy;
if(dummy=="<PP_HEADER>")
@@ -1044,7 +1044,7 @@ if ( ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_MESH>") )
+ if ( ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_MESH>") )
{
read_pseudo_mesh(ifs);
ModuleBase::GlobalFunc::SCAN_END(ifs, "</PP_MESH>");
@@ -1052,7 +1052,7 @@ if (this->nlcc)
+ if (this->nlcc)
{
ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_NLCC>");
read_pseudo_nlcc(ifs);
@@ -1061,12 +1061,12 @@ ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_LOCAL>");
+ ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_LOCAL>");
read_pseudo_local(ifs);
ModuleBase::GlobalFunc::SCAN_END(ifs, "</PP_LOCAL>");
与 类似的还有 , , , 从 则可以读取旋轨耦合相关信息：
-if (has_so)
+ if (has_so)
{
ModuleBase::GlobalFunc::SCAN_BEGIN (ifs,"<PP_ADDINFO>");
read_pseudo_so (ifs);
@@ -1140,7 +1140,7 @@ if(error==0)
+ if(error==0)
{
if(this->atoms[i].flag_empty_element) upf.set_empty_element();
error_ap = upf.average_p(GlobalV::soc_lambda);
@@ -1148,7 +1148,7 @@ if(GlobalV::MY_RANK==0)
+ if(GlobalV::MY_RANK==0)
{
atoms[i].ncpp.set_pseudo_nc( upf );
....
@@ -1178,7 +1178,7 @@ }
该函数属于类 pseudo_nc，而 pseudo_nc 对象为 atom 的数据成员，atoms 则为 UnitCell 的数据成员。pseudo_nc::set_pseudo_h()，pseudo_nc::set_pseudo_atom 和 pseudo_nc::set_pseudo_vl 的内容在此省略，但其分别为将 Hamilton, 原子性质和 Vlocal 相关数据从 upf 对象拷贝。之后(1)使用 lll 刷新为 upf 对象的 projectors 的角动量，然后计算出磁角动量区分时的 projector 个数。(2)取所有 projector 衰减到 0 时候的最大最普适半径。
-# 赝势信息后处理
+赝势信息后处理
回到 module_cell/unitcell.cpp line 663，接下来为每个原子创建目录，在目录中写 [原子label].NONLOCAL 文件。[label].NONLOCAL 文件中内容包含 <HEADER>, <DIJ> 和 <PP_BETA> 三个 tag。
<HEADER> 中包含内容：
ofs << "<HEADER>" << std::endl;
@@ -1222,21 +1222,61 @@ }
ofs << "</PP_BETA>" << std::endl;
-# 赝势信息分发：UnitCell::bcast_unitcell2(void)
+赝势信息分发：UnitCell::bcast_unitcell2(void)
#ifdef __MPI
+接下来对赝势信息进行MPI进程（processor）间的分发：
+#ifdef __MPI
+ bcast_unitcell2();
+#endif
+
+// module_cell/unitcell.cpp:bcast_unitcell2()
+void UnitCell::bcast_unitcell2(void)
+{
+ for (int i = 0; i < ntype; i++)
+ {
+ atoms[i].bcast_atom2();
+ }
+ return;
+}
+
+// module_cell/atom_spec.cpp:Atom::bcast_atom2()
+void Atom::bcast_atom2()
+{
+ this->ncpp.bcast_atom_pseudo();
+}
+
+// module_cell/atom_pseudo.cpp::Atom_pseudo::bcast_atom_pseudo()
+void Atom_pseudo::bcast_atom_pseudo(void)
+{
+....
+ Parallel_Common::bcast_int( lmax );
+....
+ Parallel_Common::bcast_double( etotps );
+....
+ Parallel_Common::bcast_bool( tvanp );
+....
+ Parallel_Common::bcast_string( psd );
+....
+ // below two 'bcast_double' lines of codes seem to have bugs,
+ // on some computers, the code will stuck here for ever.
+ // mohan note 2021-04-28
+ Parallel_Common::bcast_double( dion.c , nbeta * nbeta);
+ Parallel_Common::bcast_double( betar.c, nr * nc );
+}
+
#endif
-# 赝势信息核对
+赝势信息核对
接下来跨原子种类检验泛函是否一致：
-for(int it=0; it<ntype; it++)
+ for(int it=0; it<ntype; it++)
{
if(atoms[0].ncpp.xc_func !=atoms[it].ncpp.xc_func)
{
-# STRU 结构检查：UnitCell::check_structure()
+STRU 结构检查：UnitCell::check_structure()
检验结构中任意两原子之间距离是否大于其固定倍数（<1）的共价半径和，
-check_structure(GlobalV::MIN_DIST_COEF);
+ check_structure(GlobalV::MIN_DIST_COEF);
-# 计算轨道数：UnitCell::cal_natomwfc()
+计算轨道数：UnitCell::cal_natomwfc()
UnitCell::cal_natomwfc() 函数计算所有种类的原子轨道数量加和，对于非 nspin=4，即非 soc（自旋轨道耦合）情况，角量子数 l 和 s 非耦合，l 单独可以作为好的量子数来区分量子态，因此对于每个赝势中定义的 wfc，若其对应 occupation 大于等于 0（即有效 wfc），则对应于其角量子数 l，轨道数量增加 2l+1，即计数其磁量子数 m，也相当于对 alpha 和 beta spin 的单独计数。对于 nspin=4 的情况，若考虑 soc，则轨道数对 j=l+s 的情况，当前原子种类当前角量子数对应轨道数量记为 2l+1+1，否则为 2l+1。对于非 soc 但 nspin=4，当前原子种类轨道当前角量子数对应轨道数量记(2l+1)*2：
void UnitCell::cal_natomwfc(std::ofstream &log)
{
@@ -1291,9 +1331,9 @@ 计算跨原子种类最大角量子数 UnitCell::lmax 和某 l 对应最大 zeta 数 UnitCell::nmax，以及跨原子种类的类内 zeta 数总和最大值 UnitCell::nmax_total
寻找赝势中最大角量子数 UnitCell::lmax_ppwf。
-# 价电子数核对
+价电子数核对
核对赝势中定义的价电子数与 ABACUS 预置库中原子的最小价电子数
-# 获取最大格点数量：UnitCell::cal_meshx()
+获取最大格点数量：UnitCell::cal_meshx()
计算跨原子种类的最大格点数量，存储在 UnitCell::meshx 中，目前 ABACUS 代码中变量命名后缀 x 可能代表 max，正如之前看到 npwx 等。
至此，我们离开函数 UnitCell::read_pseudo()，回到 ModuleESolver::ESolver_FP::Init() 函数。
@@ -1304,7 +1344,7 @@ Introduction to ABACUS: Path to PW calculation - Part 2
下篇：Introduction to ABACUS: Path to PW calculation - Part 4
@@ -1348,7 +1388,7 @@ No results matching "
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采用PBE交换关联泛函和自旋极化得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出不加电场时，两个自旋方向的能带图几乎一样，都有带隙。","alt":"采用PBE交换关联泛函和自旋极化得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出不加电场时，两个自旋方向的能带图几乎一样，都有带隙。","nro":12,"url":"picture/fig_surface5-4.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"采用PBE交换关联泛函和自旋极化得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出不加电场时，两个自旋方向的能带图几乎一样，都有带隙。","attributes":{},"skip":false,"key":"1.1.15.4"},{"backlink":"abacus-surface5.html#fig1.1.15.5","level":"1.1.15","list_caption":"Figure: 采用PBE交换关联泛函和自旋极化，再给体系加上0.1 V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","alt":"采用PBE交换关联泛函和自旋极化，再给体系加上0.1 V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","nro":13,"url":"picture/fig_surface5-5.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"采用PBE交换关联泛函和自旋极化，再给体系加上0.1 V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","attributes":{},"skip":false,"key":"1.1.15.5"},{"backlink":"abacus-surface6.html#fig1.1.16.1","level":"1.1.16","list_caption":"Figure: 一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","alt":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","nro":14,"url":"picture/fig_surface6-1.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","attributes":{},"skip":false,"key":"1.1.16.1"},{"backlink":"abacus-surface6.html#fig1.1.16.2","level":"1.1.16","list_caption":"Figure: 静电势（Electrostatic Potential）沿超胞Z轴变化图","alt":"静电势（Electrostatic Potential）沿超胞Z轴变化图","nro":15,"url":"picture/fig_surface6-2.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"静电势（Electrostatic Potential）沿超胞Z轴变化图","attributes":{},"skip":false,"key":"1.1.16.2"},{"backlink":"develop-path4.html#fig1.2.9.1","level":"1.2.9","list_caption":"Figure: ","alt":" ","nro":16,"url":"picture/fig_path4-1.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":" ","attributes":{},"skip":false,"key":"1.2.9.1"},{"backlink":"develop-path4.html#fig1.2.9.2","level":"1.2.9","list_caption":"Figure: PW_Basis::distribute_r()：设一个pool中有5个processors","alt":"PW_Basis::distribute_r()：设一个pool中有5个processors","nro":17,"url":"picture/fig_path4-2.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"PW_Basis::distribute_r()：设一个pool中有5个processors","attributes":{},"skip":false,"key":"1.2.9.2"},{"backlink":"develop-path4.html#fig1.2.9.3","level":"1.2.9","list_caption":"Figure: this->count_pw_st(st_length2D, st_bottom2D)","alt":"this->count_pw_st(st_length2D, st_bottom2D)","nro":18,"url":"picture/fig_path4-3.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"this->count_pw_st(st_length2D, st_bottom2D)","attributes":{},"skip":false,"key":"1.2.9.3"},{"backlink":"develop-path5.html#fig1.2.10.1","level":"1.2.10","list_caption":"Figure: 善用Ctrl+F","alt":"善用Ctrl+F","nro":19,"url":"picture/fig_path5-9.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"善用Ctrl+F","attributes":{},"skip":false,"key":"1.2.10.1"},{"backlink":"develop-path5.html#fig1.2.10.2","level":"1.2.10","list_caption":"Figure: klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","alt":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","nro":20,"url":"picture/fig_path5-10.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","attributes":{},"skip":false,"key":"1.2.10.2"},{"backlink":"develop-path5.html#fig1.2.10.3","level":"1.2.10","list_caption":"Figure: klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","alt":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","nro":21,"url":"picture/fig_path5-11.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","attributes":{},"skip":false,"key":"1.2.10.3"},{"backlink":"develop-path5.html#fig1.2.10.4","level":"1.2.10","list_caption":"Figure: 1-dimensional example","alt":"1-dimensional example","nro":22,"url":"picture/fig_path5-12.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"1-dimensional example","attributes":{},"skip":false,"key":"1.2.10.4"},{"backlink":"develop-path5.html#fig1.2.10.5","level":"1.2.10","list_caption":"Figure: 2-dimensional example","alt":"2-dimensional example","nro":23,"url":"picture/fig_path5-13.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"2-dimensional example","attributes":{},"skip":false,"key":"1.2.10.5"}]},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"develop-path3.md","mtime":"2023-10-04T15:11:45.401Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-10-04T15:29:41.868Z"},"basePath":".","book":{"language":""}});
});
diff --git a/_book/develop-path4.html b/_book/develop-path4.html
index 1840948c..2b9cddf9 100644
--- a/_book/develop-path4.html
+++ b/_book/develop-path4.html
@@ -750,14 +750,14 @@ Driver
-Driver::atomic_world()
-Driver::driver_run()
-多层继承：Init() functions in esolver class
-Trigger: ESolver_FP::Init()
-平面波格点初始化：PW_Basis:: initgrids()
+Driver
+Driver::atomic_world()
+Driver::driver_run()
+多层继承：Init() functions in esolver class
+Trigger: ESolver_FP::Init()
+平面波格点初始化：PW_Basis:: initgrids()
完成了 INPUT 和 STRU，以及赝势文件的读取环节，接下来我们来到平面波的初始化设置相关部分。
-void ESolver_FP::Init(Input& inp, UnitCell& cell)
+ void ESolver_FP::Init(Input& inp, UnitCell& cell)
{
....
if (inp.nx * inp.ny * inp.nz == 0)
@@ -782,7 +782,7 @@ virtual void initgrids(const double lat0_in,const ModuleBase::Matrix3 latvec_in,
+ virtual void initgrids(const double lat0_in,const ModuleBase::Matrix3 latvec_in,
const double gridecut)
{
// generation of nx, ny and nz are omitted here
@@ -868,7 +868,7 @@ }
❗ 注意：这里还完成了倒空间格点数量 fftnx, fftny 和 fftnz 的赋值。因为 FFT 变换前后的格点数量一般相同，因此 fftnx = nx，fftny = ny，...。
-
+图 1. 然后对平面波在 MPI 进程间进行分发：
//module_esolver/esolver_fp.cpp
void ESolver_FP::Init(Input& inp, UnitCell& cell)
@@ -889,9 +889,9 @@ ::
timer::tick(this->classname, "setuptransform");
}
-PW_Basis::setuptransform()（link）
-# 并行机制简述
-## 并行池
+PW_Basis::setuptransform()（link）
+并行机制简述
+并行池
到这里，我们不得不开始对平面波的 MPI 并行机制有一个大致的认识。在 ABACUS 中，CPU（=processor）首先根据不同的布里渊区 k 点分组被划分成不同的并行池（parallelizaiton pool），每个 pool 都包含几个 k 点，在每个 pool 里面会有完整的对该 k 点求解 Kohn-Sham 方程的过程。因此，在每个 pool 中采用一定数量的 CPU 进程来完成计算。在 INPUT 文件中，KPAR 参数决定了并行池的数量（即 pool 的个数）。换句话说，ABACUS 的 k 点并行机制为，将 k 点（设其数量为 nkpt）分配在 KPAR 个 pool 中，若一共有 nproc 个 processor，则：
- 每个 pool 有
nproc/KPAR 个 processor
@@ -899,7 +899,7 @@ ## MPI 进程编号：rank
+MPI 进程编号：rank
rank 是一个在 MPI 并行里常被用到的变量。在拥有不止一个 processor 的时候，每个 processor 都具有唯一的编号，称为 rank。如果在每个 processor 都有 rank 的基础上还定义了 pool，以及在每个 pool 中的 processor 数量，则 processor 除了有跨 pool 的全局 rank，也可以有 pool 之内的局部 rank，这部分内容见 module_base/global_variable.cpp:
int NPROC = 1;
int KPAR = 1;
@@ -926,7 +926,7 @@ }
}
-## 并行策略
+并行策略
于是问题便到来：在并行条件下，代码究竟是如何执行的？
- 对于多核 CPU，是否运行在其上的所有程序都进行了并行化？
@@ -950,9 +950,9 @@ ## OpenMP-MPI 混合编程
+OpenMP-MPI 混合编程
通常来讲，尽管 OpenMP 提供了线程并行，但由于共享内存可能并不存在于 processors 之间，或 computer, nodes 之间，且没有适合的内存共享系统（multi-socket server），此时如果以 OpenMP 放心运行，则可能得出错误结果或直接报错——因为内存无法访问。对于这种情况，需要使用 MPI（Message passing interface）来维持无内存共享处理单元之间的信息交换，以及信息分发和分布计算，而在处理单元内部，即可以共享内存的域内，则可以通过 OpenMP 技术来进行线程级并行。
-# 实空间格点分发
+实空间格点分发
在简单介绍完并行机制后，我们知道，对于未显式以并行方式实现的函数，其运行将在每一个 processor。在接下来的平面波分发过程中，请始终牢记这一理念，尤其在 processor-local 变量和 processor-global 变量的传值过程中。
稍加回溯：
void ESolver_FP::Init(Input& inp, UnitCell& cell)
@@ -968,7 +968,7 @@ ## 实空间：PW_Basis::distribute_r()
+实空间：PW_Basis::distribute_r()
❗Attention
注意，此时实际调用的也是 PW_Basis_Big 而非 PW_Basis 的 distribute_r() 函数。
@@ -1011,8 +1011,8 @@ {
....
该判断不会 always true。因此 PW_Basis::distribute_r() 将 3D 实空间格点，按照 z 方向进行分发，分给了不同的 processors，并赋值 this->npz，this->nplane, this->startz_current 和 this->nrxx，意义分别为当前 processor 的 z 方向格点数量、xy 平面数量、z 格点的起始索引以及当前 processor 所分得实空间格点总数（分配后 z 方向格点 ×xy 平面格点）。
-
-## 倒空间：PW_Basis::distribute_g()
+图 2. PW_Basis::distribute_r()：设一个pool中有5个processors 倒空间：PW_Basis::distribute_g()
倒空间格点的分发采用了和实空间不同的方式，这主要是因为倒空间“球”的存在（ecutwfc 和 ecutrho），使得非空间中所有点都需要考虑在内，而实空间则并非如此。更一般而言，有限的实空间带来无限的倒空间（即实空间 delta 函数需要无限数量的平面波展开）延展，而有限的倒空间（倒空间 delta 点）带来无限的实空间延展（如一个平面波）。
🔧重构信息
@@ -1066,7 +1066,7 @@
delete
[] st_bottom2D; delete[] st_length2D;
}
-### 分发最小单元：“棍子” - 准备工作
+分发最小单元：“棍子” - 准备工作
穿过布里渊区的整数点（2pi/a 的整数倍）都代表一个三个 index 的平面波，而一系列的点在截断半径以内沿着某个方向就组成了所谓的“stick”（代表平面波集合的“棍子”，一个“棍子”包含了多个平面波，简称就叫“棍子”）。
PW_Basis::count_pw_st() 函数（Link）计算了每个(x,y)对应的“棍子”的底部和“长度”，即对倒空间只分辨(x,y)，则会得到沿 z 方向的点的集合，被称为“棍子”。而“棍子”区域内部每一个点都代表一个平面波。“棍子”的底部对应于最小的 iz 值，“根子”的长度则为当前(x,y)所包含的平面波数量：
for (int ix = ix_start; ix <= ix_end; ++ix)
@@ -1098,7 +1098,7 @@ }
}
-
+图 3. this->count_pw_st(st_length2D, st_bottom2D) 在倒空间分发平面波时，由于 x/y/z 均等在正负半轴 span，因此常常会涉及到 C++ 不支持负数索引的问题（btw: Python 和 FORTRAN 支持负数索引，但支持方式不同），ABACUS 当前所采取的策略是：
if (x<0) x += this->nx; if (y<0) y += this->ny; if (z<0) z += this->nz;
@@ -1107,7 +1107,7 @@ ### “棍子”的分发和分发记录
+“棍子”的分发和分发记录
PW_Basis::collect_st() 和 PW_Basis::divide_sticks_1() 分别排序与分发“棍子”到不同 processor：
- 按照棍子从长到短顺序进行排序，即
st_length2D 由大到小排序，然后适用于 st_bottom2D 等变量
@@ -1136,7 +1136,7 @@ this
->nstnz = this->nst * this->nz;
....
-### 映射表：OOP？
+映射表：OOP？
在倒空间平面波的分发过程中，共建立过四个映射表，分别是 this->fftixy2ip, this->istot2ixy, this->ig2isz 和 this->is2fftixy，其意义分别为：
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diff --git a/_book/develop-path1.html b/_book/develop-path1.html
index 1de92b86..d41c1be3 100644
--- a/_book/develop-path1.html
+++ b/_book/develop-path1.html
@@ -1112,8 +1112,8 @@ <
Input_Conv::Convert()
这个函数实现了从 Input 类对象的数据成员到 GlobalV 和 GlobalC 等全局变量集合的转换。相当于从 Input 到 GlobalV 和 GlobalC，以及其他直接的类的参数上载：
-其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
+其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
void Input_Conv::Convert(void)
{
....
@@ -1308,7 +1308,7 @@
不要忘记我们已经完成 Driver::reading() 函数内容，到达 Driver::atomic_world()。这一点从本文档设置的分级目录中也可以看得到。
-cppvoid Driver::init()
+void Driver::init()
{
this->reading();
this->atomic_world(); // <- here!
@@ -1518,7 +1518,7 @@ 从 SIAB 到 ABACUS（一）：准备工作（施工中 🚧）
下篇：Introduction to ABACUS: Path to PW calculation - Part 2
@@ -1562,7 +1562,7 @@ No results matching "
var gitbook = gitbook || [];
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index 191dfe74..d829579b 100644
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@@ -1028,7 +1028,7 @@ // a(i) is lattice vector
}
-我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
+我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
UnitCell::read_atom_positions()
🔧重构思考
@@ -1042,7 +1042,7 @@
::
GlobalFunc::READ_VALUE( ifpos, Coordinate);
STRU 第二行指定坐标类型，被读取为 UnitCell::Coordinate。UnitCell::Coordinate 在 STRU 里有不同选项，⚙ 决定原子的具体位置和单位：
-if(Coordinate != "Cartesian"
+ if(Coordinate != "Cartesian"
&& Coordinate != "Direct"
&& Coordinate != "Cartesian_angstrom"
&& Coordinate != "Cartesian_au"
@@ -1092,7 +1092,7 @@ int na = 0;
+ int na = 0;
this->nat = 0;
assert(ntype>0);
for (int it = 0;it < ntype; it++)
@@ -1105,7 +1105,7 @@ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
bool sequence_match = false;
for(int it2=0; it2<ntype; it2++)
{
@@ -1121,7 +1121,7 @@ }
读取当前原子类型的 starting_magnetization、原子总数 na
-ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
...
ModuleBase::GlobalFunc::READ_VALUE(ifpos, na);
this->atoms[it].na = na;
@@ -1149,17 +1149,17 @@ [
it].m_loc_ = new ModuleBase::Vector3<double>[na];
⚙ 然后在 ATOMIC_POSITIONS 中读取：
-atoms[it].mass = this->atom_mass[it];
+ atoms[it].mass = this->atom_mass[it];
❗ 此处的 atoms[it].mass 与 this->atom_mass[it] 的用法与 atomis[it].label 与 this->atom_label[it] 不同：传值 vs 核对。
接下来读取类中每个原子的速度信息，在做分子动力学模拟的时候可能需要用到：
-for (int ia = 0;ia < na; ia++)
+ for (int ia = 0;ia < na; ia++)
{
ifpos >> v.x >> v.y >> v.z;
然而，当前 STRU 文件在 ATOMIC_POSITIONS 的设计比较复杂，其可以包括任何一组 atom-specific 数据，且数量和顺序均不受限制，这导致判断条件变得复杂，详见 module_cell/read_atoms.cpp:line 536 - 567（link）。
atoms[it].mag 的赋值并非直接读取：
-else if ( tmpid == "mag" || tmpid == "magmom")
+ else if ( tmpid == "mag" || tmpid == "magmom")
{
set_element_mag_zero = true;
double tmpamg=0; ifpos >> tmpamg;
@@ -1185,7 +1185,7 @@ }
⚙ 若 mag/magmom 后有一个值，则读取其值赋给 atoms[it]::mag[ia]，将 input_vec_mag 置为 false，若有三个值，则三个值依次被传入 atoms[it].m_loc_[ia].x, atoms[it].m_loc_[ia].y 和 atoms[it].m_loc_[ia].z，并将 input_vec_mag 置为 true，之后其向量模长为 atoms[it]::mag[ia]，然后在使用 angle1, angle2 来重新生成 mag。
-if(GlobalV::NSPIN==4)
+ if(GlobalV::NSPIN==4)
{
if(GlobalV::NONCOLIN)
{
@@ -1227,7 +1227,7 @@ pw.x input description
ABACUS 对 nspin=4 情况的参数处理：
//module_io/input_conv.cpp line 376
if (INPUT.noncolin || INPUT.lspinorb)
@@ -1312,7 +1312,7 @@
UnitCell::setup_cell(): the rest, and an example of backtracking unclear variable
离开 STRU 文件的解析部分，接下来计算了初始磁化强度：
-//after read STRU, calculate initial total magnetization when NSPIN=2
+ //after read STRU, calculate initial total magnetization when NSPIN=2
if(GlobalV::NSPIN == 2 && !GlobalV::TWO_EFERMI)
{
for(int it = 0;it<this->ntype; it++)
@@ -1326,31 +1326,25 @@ if (std::abs(INPUT.nupdown) > 1e-6)
- {
- GlobalV::TWO_EFERMI = true;
- GlobalV::nupdown = INPUT.nupdown;
- }
-
-因此 GlobalV::TWO_EFERMI 变量实际依赖于 INPUT.nupdown。
-
-- 接下来在
module_io/input.cpp 中寻找含 INPUT.nupdown 的 if(strcmp(...)) 单元，查看在 INPUT 文件中是何参数赋予其具体值：
-
-else if (strcmp("nupdown", word) == 0)
+在 module_io/input_conv.cpp 中寻找该变量，是何变量赋其值，发现： if (std::abs(INPUT.nupdown) > 1e-6)
{
- read_value(ifs, nupdown);
- }
+ GlobalV::TWO_EFERMI = true;
+ GlobalV::nupdown = INPUT.nupdown;
+ }
-即 INPUT.nupdown 在 INPUT 中也为 nupdown。接下来打开 Full keyword list 寻找其解释。
-
+ 因此 GlobalV::TWO_EFERMI 变量实际依赖于 INPUT.nupdown。
+接下来在 module_io/input.cpp 中寻找含 INPUT.nupdown 的 if(strcmp(...)) 单元，查看在 INPUT 文件中是何参数赋予其具体值： else if (strcmp("nupdown", word) == 0)
+ {
+ read_value(ifs, nupdown);
+ }
+
+即 INPUT.nupdown 在 INPUT 中也为 nupdown。接下来打开 Full keyword list 寻找其解释。
得到结果，即 nupdown 为 spin up 和 spin down 电子数量差值：
因此该部分逻辑为：若未使用 nupdown 来指定单电子数量，则对每种原子内每个原子，累加其 mag/magmom，即磁矩模长，赋予 GlobalV::nupdown。❗ 但对于两种方式均赋予，但值不一致的情况未进行处理。
接下来根据在 STRU 中读取的晶胞参数，计算晶胞体积，并计算倒空间矢量（在上篇中已经对 latvec, G, GT, GGT 有所介绍，invGGT 的意义也不言自明）：
-this->omega = std::abs( latvec.Det() ) * this->lat0 * lat0 * lat0 ;
+ this->omega = std::abs( latvec.Det() ) * this->lat0 * lat0 * lat0 ;
this->GT = latvec.Inverse();
this->G = GT.Transpose();
@@ -1442,7 +1436,7 @@ =
static_cast<ModulePW::PW_Basis_Big*>(pw_rho);
对于 ESolver 本身，其指针对象 p_esolver 实际上也有类似操作：
-//Some API to operate E_Solver
+ //Some API to operate E_Solver
void init_esolver(ESolver*& p_esolver)
{
//determine type of esolver based on INPUT information
@@ -1907,7 +1901,7 @@ Introduction to ABACUS: Path to PW calculation - Part 1
下篇：Introduction to ABACUS: Path to PW calculation - Part 3
@@ -1951,7 +1945,7 @@ No results matching "
var gitbook = gitbook || [];
gitbook.push(function() {
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st_bottom2D)","attributes":{},"skip":false,"key":"1.2.9.3"},{"backlink":"develop-path5.html#fig1.2.10.1","level":"1.2.10","list_caption":"Figure: 善用Ctrl+F","alt":"善用Ctrl+F","nro":19,"url":"picture/fig_path5-9.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"善用Ctrl+F","attributes":{},"skip":false,"key":"1.2.10.1"},{"backlink":"develop-path5.html#fig1.2.10.2","level":"1.2.10","list_caption":"Figure: klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","alt":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","nro":20,"url":"picture/fig_path5-10.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","attributes":{},"skip":false,"key":"1.2.10.2"},{"backlink":"develop-path5.html#fig1.2.10.3","level":"1.2.10","list_caption":"Figure: klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","alt":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","nro":21,"url":"picture/fig_path5-11.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","attributes":{},"skip":false,"key":"1.2.10.3"},{"backlink":"develop-path5.html#fig1.2.10.4","level":"1.2.10","list_caption":"Figure: 1-dimensional example","alt":"1-dimensional example","nro":22,"url":"picture/fig_path5-12.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"1-dimensional example","attributes":{},"skip":false,"key":"1.2.10.4"},{"backlink":"develop-path5.html#fig1.2.10.5","level":"1.2.10","list_caption":"Figure: 2-dimensional example","alt":"2-dimensional example","nro":23,"url":"picture/fig_path5-13.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"2-dimensional example","attributes":{},"skip":false,"key":"1.2.10.5"}]},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"develop-path2.md","mtime":"2023-10-04T14:37:12.149Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-10-04T15:29:41.868Z"},"basePath":".","book":{"language":""}});
});
diff --git a/_book/develop-path3.html b/_book/develop-path3.html
index b8de33d9..09176394 100644
--- a/_book/develop-path3.html
+++ b/_book/develop-path3.html
@@ -750,11 +750,11 @@ Driver
-Driver::atomic_world()
-Driver::driver_run()
-多层继承：Init() functions in esolver class
-Trigger: ESolver_FP::Init()
+Driver
+Driver::atomic_world()
+Driver::driver_run()
+多层继承：Init() functions in esolver class
+Trigger: ESolver_FP::Init()
承接上篇中已经导入的结构信息，以及了解到构造函数及其伴随的变量初始化和 ABACUS 里应用到的 C++ 多态编程，接下来即将（逐渐）步入 ABACUS 的核心内容。我们暂时跳过位于 source/driver_run.cpp:driver_run() 的：
// 3. For these two types of calculations
// nothing else need to be initialized
@@ -830,14 +830,14 @@ }
同理，ESolver_KS 的数据成员，也被 ESolver_KS_PW 继承。ESolver_FP::Init() 首先调用 UnitCell::read_pseudo() 函数进行赝势文件读取，而将赝势文件读取任务放在 FP 层级下，也暗示对于 ABACUS 的第一性原理方法实现来讲，都需要使用赝势。
-Pseudopotential import: UnitCell::read_pseudo()
+Pseudopotential import: UnitCell::read_pseudo()
void UnitCell::read_pseudo(std::ofstream &ofs)
{
read_cell_pseudopots(GlobalV::global_pseudo_dir, ofs);
在解读赝势文件读取功能之前，首先需要对赝势文件的结构和信息做一定程度的了解。
-# ONCV pseudopotential file
-## Section 0: Norm-conserving conditions, generation of pseudopotential and header of exact UPF file
+ONCV pseudopotential file
+Section 0: Norm-conserving conditions, generation of pseudopotential and header of exact UPF file
赝势的意义不言自明，其中模守恒赝势需满足如下条件：
- （赝势得到的能级和全电子方法求解的能级一样，这里 ps 代表 pseudopotentials）
@@ -852,7 +852,7 @@ V_l(r)=\frac{1}{\phi^\text{ps}_l(r)}[\epsilon^\text{ps}_l-\frac{\hbar^2}{2m}\frac{l(l+1)}{r^2}+\frac{\hbar^2}{2m}\frac{d^2}{dr^2}]\phi^\text{ps}_l(r)，解得。
- 扣除中 Hartree、xc 部分，得到：。
-更多细节见
+更多细节见：www.tcm.phy.cam.ac.uk
<UPF version="2.0.1">
<PP_INFO>
<!-- omitted information here -->
@@ -865,8 +865,8 @@ <!-- -->
从 UPF 文件（注意 UPF 文件也有不同的版本，目前 ABACUS 都支持，若有不支持的，可以提 Github 的 issues 进行讨论）开始，截止到 <PP_HEADER> 之前，提供了赝势文件的作者信息，引用信息以及生成赝势文件所使用的程序和相应输入文件，并附带输入文件参数中的解释。由于此块内容对实际计算并不起作用，因此暂时略过。
-## Section 1:
-<PP_HEADER
+Section 1:
+ <PP_HEADER
generated="Generated using ONCVPSP code by D. R. Hamann" author="Martin Schlipf and Francois Gygi"
date="150105" comment=""
element="Al"
@@ -890,8 +890,8 @@ number_of_proj
="4"/>
<PP_HEADER> 部分尽管已经位于所谓“not human readable”区域，但也并非如此。这部分“标签”（HTML 语境）/block 实际上包含了众多精简过的信息，如元素名称（element）、赝势类型（pseudo_type，模守恒，norm-conserving，NC），相对论效应（relativistic），是否为超软赝势等等信息。当前 Al 理论上其原子序数 13，因此有 13 个电子，但此处 z_valence 参数为 11，即有两个 1s 电子被赝化，只留下 2s, 2p, 3s, 3p 电子共 2+6+2+1 个。对于某些元素，甚至有大核赝势与小核赝势之分，根据赝化电子数量不同进行区分。显而易见地，赝化电子数量越多，则计算量越小，但计算结果的精确程度可能更低。
-## Section 2:
-<PP_MESH>
+Section 2:
+ <PP_MESH>
<PP_R type="real" size=" 602" columns="8">
0.0000 0.0100 0.0200 0.0300 0.0400 0.0500 0.0600 0.0700
<!-- omitted information here -->
@@ -907,8 +907,8 @@ </PP_MESH>
这部分开始出现了关于实空间格点相关量的定义。在 tag 中不仅指定数据类型为实数，也指定当前数据的长度（size），以及数据存储的列数（columns = 8）。PP_R 为格点坐标，PP_RAB 则为格点间距。
-## Section 3:
-<PP_LOCAL type="real" size=" 602" columns="4">
+Section 3:
+ <PP_LOCAL type="real" size=" 602" columns="4">
-4.5793174225E+01 -4.5788454271E+01 -4.5774276797E+01 -4.5750659428E+01
<!-- omitted information here -->
-3.6912752197E+00 -3.6850921941E+00 -3.6789298138E+00 -3.6727880140E+00
@@ -917,8 +917,8 @@ <PP_LOCAL>
部分开始，正式开始写入赝势的具体数值，建立在 <PP_R> 和 <PP_RAB> 所描述的实空间格点上。。<PP_LOCAL> 正是赝势的局域势部分。
-## Section 4:
-<PP_NONLOCAL>
+Section 4:
+ <PP_NONLOCAL>
<PP_BETA.1
type="real"
size=" 602"
@@ -938,8 +938,8 @@ cutoff_radius_index
=" 246" cutoff_radius=" 2.4500000000E+00" >
<!-- omitted information here -->
</PP_BETA.2>
- <PP_BETA.3 type="real" size=" 602" columns="4" index="3" angular_momentum="1"<strong>
-</strong> cutoff_radius_index=" 246" cutoff_radius=" 2.4500000000E+00" >
+ <PP_BETA.3 type="real" size=" 602" columns="4" index="3" angular_momentum="1"
+ cutoff_radius_index=" 246" cutoff_radius=" 2.4500000000E+00" >
<!-- omitted information here -->
</PP_BETA.3>
<PP_BETA.4 type="real" size=" 602" columns="4" index="4" angular_momentum="1"
@@ -956,7 +956,7 @@ \hat{V}^\text{NL}=\sum_{ij}{|\beta_i\rangle D_{ij}\langle\beta_j|}。其中一般被称为非局域势投影子（projector）。
-## Section 5: and
+Section 5: and
<PP_PSWFC>
</PP_PSWFC>
<PP_RHOATOM type="real" size=" 602" columns="4">
@@ -975,7 +975,7 @@ |\beta\rangle和 pswfc 已经乘径向坐标。
-# UnitCell::read_cell_pseudopots()
+UnitCell::read_cell_pseudopots()
link to Github -> link
void UnitCell::read_cell_pseudopots(const std::string &pp_dir, std::ofstream &log)
{
@@ -1030,7 +1030,7 @@ while (ifs.good())
+ while (ifs.good())
{
ifs >> dummy;
if(dummy=="<PP_HEADER>")
@@ -1044,7 +1044,7 @@ if ( ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_MESH>") )
+ if ( ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_MESH>") )
{
read_pseudo_mesh(ifs);
ModuleBase::GlobalFunc::SCAN_END(ifs, "</PP_MESH>");
@@ -1052,7 +1052,7 @@ if (this->nlcc)
+ if (this->nlcc)
{
ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_NLCC>");
read_pseudo_nlcc(ifs);
@@ -1061,12 +1061,12 @@ ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_LOCAL>");
+ ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_LOCAL>");
read_pseudo_local(ifs);
ModuleBase::GlobalFunc::SCAN_END(ifs, "</PP_LOCAL>");
与 类似的还有 , , , 从 则可以读取旋轨耦合相关信息：
-if (has_so)
+ if (has_so)
{
ModuleBase::GlobalFunc::SCAN_BEGIN (ifs,"<PP_ADDINFO>");
read_pseudo_so (ifs);
@@ -1140,7 +1140,7 @@ if(error==0)
+ if(error==0)
{
if(this->atoms[i].flag_empty_element) upf.set_empty_element();
error_ap = upf.average_p(GlobalV::soc_lambda);
@@ -1148,7 +1148,7 @@ if(GlobalV::MY_RANK==0)
+ if(GlobalV::MY_RANK==0)
{
atoms[i].ncpp.set_pseudo_nc( upf );
....
@@ -1178,7 +1178,7 @@ }
该函数属于类 pseudo_nc，而 pseudo_nc 对象为 atom 的数据成员，atoms 则为 UnitCell 的数据成员。pseudo_nc::set_pseudo_h()，pseudo_nc::set_pseudo_atom 和 pseudo_nc::set_pseudo_vl 的内容在此省略，但其分别为将 Hamilton, 原子性质和 Vlocal 相关数据从 upf 对象拷贝。之后(1)使用 lll 刷新为 upf 对象的 projectors 的角动量，然后计算出磁角动量区分时的 projector 个数。(2)取所有 projector 衰减到 0 时候的最大最普适半径。
-# 赝势信息后处理
+赝势信息后处理
回到 module_cell/unitcell.cpp line 663，接下来为每个原子创建目录，在目录中写 [原子label].NONLOCAL 文件。[label].NONLOCAL 文件中内容包含 <HEADER>, <DIJ> 和 <PP_BETA> 三个 tag。
<HEADER> 中包含内容：
ofs << "<HEADER>" << std::endl;
@@ -1222,21 +1222,61 @@ }
ofs << "</PP_BETA>" << std::endl;
-# 赝势信息分发：UnitCell::bcast_unitcell2(void)
+赝势信息分发：UnitCell::bcast_unitcell2(void)
#ifdef __MPI
+接下来对赝势信息进行MPI进程（processor）间的分发：
+#ifdef __MPI
+ bcast_unitcell2();
+#endif
+
+// module_cell/unitcell.cpp:bcast_unitcell2()
+void UnitCell::bcast_unitcell2(void)
+{
+ for (int i = 0; i < ntype; i++)
+ {
+ atoms[i].bcast_atom2();
+ }
+ return;
+}
+
+// module_cell/atom_spec.cpp:Atom::bcast_atom2()
+void Atom::bcast_atom2()
+{
+ this->ncpp.bcast_atom_pseudo();
+}
+
+// module_cell/atom_pseudo.cpp::Atom_pseudo::bcast_atom_pseudo()
+void Atom_pseudo::bcast_atom_pseudo(void)
+{
+....
+ Parallel_Common::bcast_int( lmax );
+....
+ Parallel_Common::bcast_double( etotps );
+....
+ Parallel_Common::bcast_bool( tvanp );
+....
+ Parallel_Common::bcast_string( psd );
+....
+ // below two 'bcast_double' lines of codes seem to have bugs,
+ // on some computers, the code will stuck here for ever.
+ // mohan note 2021-04-28
+ Parallel_Common::bcast_double( dion.c , nbeta * nbeta);
+ Parallel_Common::bcast_double( betar.c, nr * nc );
+}
+
#endif
-# 赝势信息核对
+赝势信息核对
接下来跨原子种类检验泛函是否一致：
-for(int it=0; it<ntype; it++)
+ for(int it=0; it<ntype; it++)
{
if(atoms[0].ncpp.xc_func !=atoms[it].ncpp.xc_func)
{
-# STRU 结构检查：UnitCell::check_structure()
+STRU 结构检查：UnitCell::check_structure()
检验结构中任意两原子之间距离是否大于其固定倍数（<1）的共价半径和，
-check_structure(GlobalV::MIN_DIST_COEF);
+ check_structure(GlobalV::MIN_DIST_COEF);
-# 计算轨道数：UnitCell::cal_natomwfc()
+计算轨道数：UnitCell::cal_natomwfc()
UnitCell::cal_natomwfc() 函数计算所有种类的原子轨道数量加和，对于非 nspin=4，即非 soc（自旋轨道耦合）情况，角量子数 l 和 s 非耦合，l 单独可以作为好的量子数来区分量子态，因此对于每个赝势中定义的 wfc，若其对应 occupation 大于等于 0（即有效 wfc），则对应于其角量子数 l，轨道数量增加 2l+1，即计数其磁量子数 m，也相当于对 alpha 和 beta spin 的单独计数。对于 nspin=4 的情况，若考虑 soc，则轨道数对 j=l+s 的情况，当前原子种类当前角量子数对应轨道数量记为 2l+1+1，否则为 2l+1。对于非 soc 但 nspin=4，当前原子种类轨道当前角量子数对应轨道数量记(2l+1)*2：
void UnitCell::cal_natomwfc(std::ofstream &log)
{
@@ -1291,9 +1331,9 @@ 计算跨原子种类最大角量子数 UnitCell::lmax 和某 l 对应最大 zeta 数 UnitCell::nmax，以及跨原子种类的类内 zeta 数总和最大值 UnitCell::nmax_total
寻找赝势中最大角量子数 UnitCell::lmax_ppwf。
-# 价电子数核对
+价电子数核对
核对赝势中定义的价电子数与 ABACUS 预置库中原子的最小价电子数
-# 获取最大格点数量：UnitCell::cal_meshx()
+获取最大格点数量：UnitCell::cal_meshx()
计算跨原子种类的最大格点数量，存储在 UnitCell::meshx 中，目前 ABACUS 代码中变量命名后缀 x 可能代表 max，正如之前看到 npwx 等。
至此，我们离开函数 UnitCell::read_pseudo()，回到 ModuleESolver::ESolver_FP::Init() 函数。
@@ -1304,7 +1344,7 @@ Introduction to ABACUS: Path to PW calculation - Part 2
下篇：Introduction to ABACUS: Path to PW calculation - Part 4
@@ -1348,7 +1388,7 @@ No results matching "
var gitbook = gitbook || [];
gitbook.push(function() {
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example","attributes":{},"skip":false,"key":"1.2.10.5"}]},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"develop-path3.md","mtime":"2023-10-04T15:11:45.401Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-10-04T15:29:41.868Z"},"basePath":".","book":{"language":""}});
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diff --git a/_book/develop-path4.html b/_book/develop-path4.html
index 1840948c..2b9cddf9 100644
--- a/_book/develop-path4.html
+++ b/_book/develop-path4.html
@@ -750,14 +750,14 @@ Driver
-Driver::atomic_world()
-Driver::driver_run()
-多层继承：Init() functions in esolver class
-Trigger: ESolver_FP::Init()
-平面波格点初始化：PW_Basis:: initgrids()
+Driver
+Driver::atomic_world()
+Driver::driver_run()
+多层继承：Init() functions in esolver class
+Trigger: ESolver_FP::Init()
+平面波格点初始化：PW_Basis:: initgrids()
完成了 INPUT 和 STRU，以及赝势文件的读取环节，接下来我们来到平面波的初始化设置相关部分。
-void ESolver_FP::Init(Input& inp, UnitCell& cell)
+ void ESolver_FP::Init(Input& inp, UnitCell& cell)
{
....
if (inp.nx * inp.ny * inp.nz == 0)
@@ -782,7 +782,7 @@ virtual void initgrids(const double lat0_in,const ModuleBase::Matrix3 latvec_in,
+ virtual void initgrids(const double lat0_in,const ModuleBase::Matrix3 latvec_in,
const double gridecut)
{
// generation of nx, ny and nz are omitted here
@@ -868,7 +868,7 @@ }
❗ 注意：这里还完成了倒空间格点数量 fftnx, fftny 和 fftnz 的赋值。因为 FFT 变换前后的格点数量一般相同，因此 fftnx = nx，fftny = ny，...。
-
+图 1. 然后对平面波在 MPI 进程间进行分发：
//module_esolver/esolver_fp.cpp
void ESolver_FP::Init(Input& inp, UnitCell& cell)
@@ -889,9 +889,9 @@ ::
timer::tick(this->classname, "setuptransform");
}
-PW_Basis::setuptransform()（link）
-# 并行机制简述
-## 并行池
+PW_Basis::setuptransform()（link）
+并行机制简述
+并行池
到这里，我们不得不开始对平面波的 MPI 并行机制有一个大致的认识。在 ABACUS 中，CPU（=processor）首先根据不同的布里渊区 k 点分组被划分成不同的并行池（parallelizaiton pool），每个 pool 都包含几个 k 点，在每个 pool 里面会有完整的对该 k 点求解 Kohn-Sham 方程的过程。因此，在每个 pool 中采用一定数量的 CPU 进程来完成计算。在 INPUT 文件中，KPAR 参数决定了并行池的数量（即 pool 的个数）。换句话说，ABACUS 的 k 点并行机制为，将 k 点（设其数量为 nkpt）分配在 KPAR 个 pool 中，若一共有 nproc 个 processor，则：
- 每个 pool 有
nproc/KPAR 个 processor
@@ -899,7 +899,7 @@ ## MPI 进程编号：rank
+MPI 进程编号：rank
rank 是一个在 MPI 并行里常被用到的变量。在拥有不止一个 processor 的时候，每个 processor 都具有唯一的编号，称为 rank。如果在每个 processor 都有 rank 的基础上还定义了 pool，以及在每个 pool 中的 processor 数量，则 processor 除了有跨 pool 的全局 rank，也可以有 pool 之内的局部 rank，这部分内容见 module_base/global_variable.cpp:
int NPROC = 1;
int KPAR = 1;
@@ -926,7 +926,7 @@ }
}
-## 并行策略
+并行策略
于是问题便到来：在并行条件下，代码究竟是如何执行的？
- 对于多核 CPU，是否运行在其上的所有程序都进行了并行化？
@@ -950,9 +950,9 @@ ## OpenMP-MPI 混合编程
+OpenMP-MPI 混合编程
通常来讲，尽管 OpenMP 提供了线程并行，但由于共享内存可能并不存在于 processors 之间，或 computer, nodes 之间，且没有适合的内存共享系统（multi-socket server），此时如果以 OpenMP 放心运行，则可能得出错误结果或直接报错——因为内存无法访问。对于这种情况，需要使用 MPI（Message passing interface）来维持无内存共享处理单元之间的信息交换，以及信息分发和分布计算，而在处理单元内部，即可以共享内存的域内，则可以通过 OpenMP 技术来进行线程级并行。
-# 实空间格点分发
+实空间格点分发
在简单介绍完并行机制后，我们知道，对于未显式以并行方式实现的函数，其运行将在每一个 processor。在接下来的平面波分发过程中，请始终牢记这一理念，尤其在 processor-local 变量和 processor-global 变量的传值过程中。
稍加回溯：
void ESolver_FP::Init(Input& inp, UnitCell& cell)
@@ -968,7 +968,7 @@ ## 实空间：PW_Basis::distribute_r()
+实空间：PW_Basis::distribute_r()
❗Attention
注意，此时实际调用的也是 PW_Basis_Big 而非 PW_Basis 的 distribute_r() 函数。
@@ -1011,8 +1011,8 @@ {
....
该判断不会 always true。因此 PW_Basis::distribute_r() 将 3D 实空间格点，按照 z 方向进行分发，分给了不同的 processors，并赋值 this->npz，this->nplane, this->startz_current 和 this->nrxx，意义分别为当前 processor 的 z 方向格点数量、xy 平面数量、z 格点的起始索引以及当前 processor 所分得实空间格点总数（分配后 z 方向格点 ×xy 平面格点）。
-
-## 倒空间：PW_Basis::distribute_g()
+图 2. PW_Basis::distribute_r()：设一个pool中有5个processors 倒空间：PW_Basis::distribute_g()
倒空间格点的分发采用了和实空间不同的方式，这主要是因为倒空间“球”的存在（ecutwfc 和 ecutrho），使得非空间中所有点都需要考虑在内，而实空间则并非如此。更一般而言，有限的实空间带来无限的倒空间（即实空间 delta 函数需要无限数量的平面波展开）延展，而有限的倒空间（倒空间 delta 点）带来无限的实空间延展（如一个平面波）。
🔧重构信息
@@ -1066,7 +1066,7 @@
delete
[] st_bottom2D; delete[] st_length2D;
}
-### 分发最小单元：“棍子” - 准备工作
+分发最小单元：“棍子” - 准备工作
穿过布里渊区的整数点（2pi/a 的整数倍）都代表一个三个 index 的平面波，而一系列的点在截断半径以内沿着某个方向就组成了所谓的“stick”（代表平面波集合的“棍子”，一个“棍子”包含了多个平面波，简称就叫“棍子”）。
PW_Basis::count_pw_st() 函数（Link）计算了每个(x,y)对应的“棍子”的底部和“长度”，即对倒空间只分辨(x,y)，则会得到沿 z 方向的点的集合，被称为“棍子”。而“棍子”区域内部每一个点都代表一个平面波。“棍子”的底部对应于最小的 iz 值，“根子”的长度则为当前(x,y)所包含的平面波数量：
for (int ix = ix_start; ix <= ix_end; ++ix)
@@ -1098,7 +1098,7 @@ }
}
-
+图 3. this->count_pw_st(st_length2D, st_bottom2D) 在倒空间分发平面波时，由于 x/y/z 均等在正负半轴 span，因此常常会涉及到 C++ 不支持负数索引的问题（btw: Python 和 FORTRAN 支持负数索引，但支持方式不同），ABACUS 当前所采取的策略是：
if (x<0) x += this->nx; if (y<0) y += this->ny; if (z<0) z += this->nz;
@@ -1107,7 +1107,7 @@ ### “棍子”的分发和分发记录
+“棍子”的分发和分发记录
PW_Basis::collect_st() 和 PW_Basis::divide_sticks_1() 分别排序与分发“棍子”到不同 processor：
- 按照棍子从长到短顺序进行排序，即
st_length2D 由大到小排序，然后适用于 st_bottom2D 等变量
@@ -1136,7 +1136,7 @@ this
->nstnz = this->nst * this->nz;
....
-### 映射表：OOP？
+映射表：OOP？
在倒空间平面波的分发过程中，共建立过四个映射表，分别是 this->fftixy2ip, this->istot2ixy, this->ig2isz 和 this->is2fftixy，其意义分别为：
No results matching "
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diff --git a/_book/develop-path1.html b/_book/develop-path1.html
index 1de92b86..d41c1be3 100644
--- a/_book/develop-path1.html
+++ b/_book/develop-path1.html
@@ -1112,8 +1112,8 @@ <
Input_Conv::Convert()
这个函数实现了从 Input 类对象的数据成员到 GlobalV 和 GlobalC 等全局变量集合的转换。相当于从 Input 到 GlobalV 和 GlobalC，以及其他直接的类的参数上载：
-其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
+其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
void Input_Conv::Convert(void)
{
....
@@ -1308,7 +1308,7 @@
不要忘记我们已经完成 Driver::reading() 函数内容，到达 Driver::atomic_world()。这一点从本文档设置的分级目录中也可以看得到。
-cppvoid Driver::init()
+void Driver::init()
{
this->reading();
this->atomic_world(); // <- here!
@@ -1518,7 +1518,7 @@ 从 SIAB 到 ABACUS（一）：准备工作（施工中 🚧）
下篇：Introduction to ABACUS: Path to PW calculation - Part 2
@@ -1562,7 +1562,7 @@ No results matching "
var gitbook = gitbook || [];
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index 191dfe74..d829579b 100644
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@@ -1028,7 +1028,7 @@ // a(i) is lattice vector
}
-我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
+我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
UnitCell::read_atom_positions()
🔧重构思考
@@ -1042,7 +1042,7 @@
::
GlobalFunc::READ_VALUE( ifpos, Coordinate);
STRU 第二行指定坐标类型，被读取为 UnitCell::Coordinate。UnitCell::Coordinate 在 STRU 里有不同选项，⚙ 决定原子的具体位置和单位：
-if(Coordinate != "Cartesian"
+ if(Coordinate != "Cartesian"
&& Coordinate != "Direct"
&& Coordinate != "Cartesian_angstrom"
&& Coordinate != "Cartesian_au"
@@ -1092,7 +1092,7 @@ int na = 0;
+ int na = 0;
this->nat = 0;
assert(ntype>0);
for (int it = 0;it < ntype; it++)
@@ -1105,7 +1105,7 @@ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
bool sequence_match = false;
for(int it2=0; it2<ntype; it2++)
{
@@ -1121,7 +1121,7 @@ }
读取当前原子类型的 starting_magnetization、原子总数 na
-ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
...
ModuleBase::GlobalFunc::READ_VALUE(ifpos, na);
this->atoms[it].na = na;
@@ -1149,17 +1149,17 @@ [
it].m_loc_ = new ModuleBase::Vector3<double>[na];
⚙ 然后在 ATOMIC_POSITIONS 中读取：
-atoms[it].mass = this->atom_mass[it];
+ atoms[it].mass = this->atom_mass[it];
❗ 此处的 atoms[it].mass 与 this->atom_mass[it] 的用法与 atomis[it].label 与 this->atom_label[it] 不同：传值 vs 核对。
接下来读取类中每个原子的速度信息，在做分子动力学模拟的时候可能需要用到：
-for (int ia = 0;ia < na; ia++)
+ for (int ia = 0;ia < na; ia++)
{
ifpos >> v.x >> v.y >> v.z;
然而，当前 STRU 文件在 ATOMIC_POSITIONS 的设计比较复杂，其可以包括任何一组 atom-specific 数据，且数量和顺序均不受限制，这导致判断条件变得复杂，详见 module_cell/read_atoms.cpp:line 536 - 567（link）。
atoms[it].mag 的赋值并非直接读取：
-else if ( tmpid == "mag" || tmpid == "magmom")
+ else if ( tmpid == "mag" || tmpid == "magmom")
{
set_element_mag_zero = true;
double tmpamg=0; ifpos >> tmpamg;
@@ -1185,7 +1185,7 @@ }
⚙ 若 mag/magmom 后有一个值，则读取其值赋给 atoms[it]::mag[ia]，将 input_vec_mag 置为 false，若有三个值，则三个值依次被传入 atoms[it].m_loc_[ia].x, atoms[it].m_loc_[ia].y 和 atoms[it].m_loc_[ia].z，并将 input_vec_mag 置为 true，之后其向量模长为 atoms[it]::mag[ia]，然后在使用 angle1, angle2 来重新生成 mag。
-if(GlobalV::NSPIN==4)
+ if(GlobalV::NSPIN==4)
{
if(GlobalV::NONCOLIN)
{
@@ -1227,7 +1227,7 @@ pw.x input description
ABACUS 对 nspin=4 情况的参数处理：
//module_io/input_conv.cpp line 376
if (INPUT.noncolin || INPUT.lspinorb)
@@ -1312,7 +1312,7 @@
UnitCell::setup_cell(): the rest, and an example of backtracking unclear variable
离开 STRU 文件的解析部分，接下来计算了初始磁化强度：
-//after read STRU, calculate initial total magnetization when NSPIN=2
+ //after read STRU, calculate initial total magnetization when NSPIN=2
if(GlobalV::NSPIN == 2 && !GlobalV::TWO_EFERMI)
{
for(int it = 0;it<this->ntype; it++)
@@ -1326,31 +1326,25 @@ if (std::abs(INPUT.nupdown) > 1e-6)
- {
- GlobalV::TWO_EFERMI = true;
- GlobalV::nupdown = INPUT.nupdown;
- }
-
-因此 GlobalV::TWO_EFERMI 变量实际依赖于 INPUT.nupdown。
-
-- 接下来在
module_io/input.cpp 中寻找含 INPUT.nupdown 的 if(strcmp(...)) 单元，查看在 INPUT 文件中是何参数赋予其具体值：
-
-else if (strcmp("nupdown", word) == 0)
+在 module_io/input_conv.cpp 中寻找该变量，是何变量赋其值，发现： if (std::abs(INPUT.nupdown) > 1e-6)
{
- read_value(ifs, nupdown);
- }
+ GlobalV::TWO_EFERMI = true;
+ GlobalV::nupdown = INPUT.nupdown;
+ }
-即 INPUT.nupdown 在 INPUT 中也为 nupdown。接下来打开 Full keyword list 寻找其解释。
-
+ 因此 GlobalV::TWO_EFERMI 变量实际依赖于 INPUT.nupdown。
+接下来在 module_io/input.cpp 中寻找含 INPUT.nupdown 的 if(strcmp(...)) 单元，查看在 INPUT 文件中是何参数赋予其具体值： else if (strcmp("nupdown", word) == 0)
+ {
+ read_value(ifs, nupdown);
+ }
+
+即 INPUT.nupdown 在 INPUT 中也为 nupdown。接下来打开 Full keyword list 寻找其解释。
得到结果，即 nupdown 为 spin up 和 spin down 电子数量差值：
因此该部分逻辑为：若未使用 nupdown 来指定单电子数量，则对每种原子内每个原子，累加其 mag/magmom，即磁矩模长，赋予 GlobalV::nupdown。❗ 但对于两种方式均赋予，但值不一致的情况未进行处理。
接下来根据在 STRU 中读取的晶胞参数，计算晶胞体积，并计算倒空间矢量（在上篇中已经对 latvec, G, GT, GGT 有所介绍，invGGT 的意义也不言自明）：
-this->omega = std::abs( latvec.Det() ) * this->lat0 * lat0 * lat0 ;
+ this->omega = std::abs( latvec.Det() ) * this->lat0 * lat0 * lat0 ;
this->GT = latvec.Inverse();
this->G = GT.Transpose();
@@ -1442,7 +1436,7 @@ =
static_cast<ModulePW::PW_Basis_Big*>(pw_rho);
对于 ESolver 本身，其指针对象 p_esolver 实际上也有类似操作：
-//Some API to operate E_Solver
+ //Some API to operate E_Solver
void init_esolver(ESolver*& p_esolver)
{
//determine type of esolver based on INPUT information
@@ -1907,7 +1901,7 @@ Introduction to ABACUS: Path to PW calculation - Part 1
下篇：Introduction to ABACUS: Path to PW calculation - Part 3
@@ -1951,7 +1945,7 @@ No results matching "
var gitbook = gitbook || [];
gitbook.push(function() {
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st_bottom2D)","attributes":{},"skip":false,"key":"1.2.9.3"},{"backlink":"develop-path5.html#fig1.2.10.1","level":"1.2.10","list_caption":"Figure: 善用Ctrl+F","alt":"善用Ctrl+F","nro":19,"url":"picture/fig_path5-9.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"善用Ctrl+F","attributes":{},"skip":false,"key":"1.2.10.1"},{"backlink":"develop-path5.html#fig1.2.10.2","level":"1.2.10","list_caption":"Figure: klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","alt":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","nro":20,"url":"picture/fig_path5-10.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","attributes":{},"skip":false,"key":"1.2.10.2"},{"backlink":"develop-path5.html#fig1.2.10.3","level":"1.2.10","list_caption":"Figure: klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","alt":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","nro":21,"url":"picture/fig_path5-11.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","attributes":{},"skip":false,"key":"1.2.10.3"},{"backlink":"develop-path5.html#fig1.2.10.4","level":"1.2.10","list_caption":"Figure: 1-dimensional example","alt":"1-dimensional example","nro":22,"url":"picture/fig_path5-12.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"1-dimensional example","attributes":{},"skip":false,"key":"1.2.10.4"},{"backlink":"develop-path5.html#fig1.2.10.5","level":"1.2.10","list_caption":"Figure: 2-dimensional example","alt":"2-dimensional example","nro":23,"url":"picture/fig_path5-13.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"2-dimensional example","attributes":{},"skip":false,"key":"1.2.10.5"}]},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"develop-path2.md","mtime":"2023-10-04T14:37:12.149Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-10-04T15:29:41.868Z"},"basePath":".","book":{"language":""}});
});
diff --git a/_book/develop-path3.html b/_book/develop-path3.html
index b8de33d9..09176394 100644
--- a/_book/develop-path3.html
+++ b/_book/develop-path3.html
@@ -750,11 +750,11 @@ Driver
-Driver::atomic_world()
-Driver::driver_run()
-多层继承：Init() functions in esolver class
-Trigger: ESolver_FP::Init()
+Driver
+Driver::atomic_world()
+Driver::driver_run()
+多层继承：Init() functions in esolver class
+Trigger: ESolver_FP::Init()
承接上篇中已经导入的结构信息，以及了解到构造函数及其伴随的变量初始化和 ABACUS 里应用到的 C++ 多态编程，接下来即将（逐渐）步入 ABACUS 的核心内容。我们暂时跳过位于 source/driver_run.cpp:driver_run() 的：
// 3. For these two types of calculations
// nothing else need to be initialized
@@ -830,14 +830,14 @@ }
同理，ESolver_KS 的数据成员，也被 ESolver_KS_PW 继承。ESolver_FP::Init() 首先调用 UnitCell::read_pseudo() 函数进行赝势文件读取，而将赝势文件读取任务放在 FP 层级下，也暗示对于 ABACUS 的第一性原理方法实现来讲，都需要使用赝势。
-Pseudopotential import: UnitCell::read_pseudo()
+Pseudopotential import: UnitCell::read_pseudo()
void UnitCell::read_pseudo(std::ofstream &ofs)
{
read_cell_pseudopots(GlobalV::global_pseudo_dir, ofs);
在解读赝势文件读取功能之前，首先需要对赝势文件的结构和信息做一定程度的了解。
-# ONCV pseudopotential file
-## Section 0: Norm-conserving conditions, generation of pseudopotential and header of exact UPF file
+ONCV pseudopotential file
+Section 0: Norm-conserving conditions, generation of pseudopotential and header of exact UPF file
赝势的意义不言自明，其中模守恒赝势需满足如下条件：
- （赝势得到的能级和全电子方法求解的能级一样，这里 ps 代表 pseudopotentials）
@@ -852,7 +852,7 @@ V_l(r)=\frac{1}{\phi^\text{ps}_l(r)}[\epsilon^\text{ps}_l-\frac{\hbar^2}{2m}\frac{l(l+1)}{r^2}+\frac{\hbar^2}{2m}\frac{d^2}{dr^2}]\phi^\text{ps}_l(r)，解得。
- 扣除中 Hartree、xc 部分，得到：。
-更多细节见
+更多细节见：www.tcm.phy.cam.ac.uk
<UPF version="2.0.1">
<PP_INFO>
<!-- omitted information here -->
@@ -865,8 +865,8 @@ <!-- -->
从 UPF 文件（注意 UPF 文件也有不同的版本，目前 ABACUS 都支持，若有不支持的，可以提 Github 的 issues 进行讨论）开始，截止到 <PP_HEADER> 之前，提供了赝势文件的作者信息，引用信息以及生成赝势文件所使用的程序和相应输入文件，并附带输入文件参数中的解释。由于此块内容对实际计算并不起作用，因此暂时略过。
-## Section 1:
-<PP_HEADER
+Section 1:
+ <PP_HEADER
generated="Generated using ONCVPSP code by D. R. Hamann" author="Martin Schlipf and Francois Gygi"
date="150105" comment=""
element="Al"
@@ -890,8 +890,8 @@ number_of_proj
="4"/>
<PP_HEADER> 部分尽管已经位于所谓“not human readable”区域，但也并非如此。这部分“标签”（HTML 语境）/block 实际上包含了众多精简过的信息，如元素名称（element）、赝势类型（pseudo_type，模守恒，norm-conserving，NC），相对论效应（relativistic），是否为超软赝势等等信息。当前 Al 理论上其原子序数 13，因此有 13 个电子，但此处 z_valence 参数为 11，即有两个 1s 电子被赝化，只留下 2s, 2p, 3s, 3p 电子共 2+6+2+1 个。对于某些元素，甚至有大核赝势与小核赝势之分，根据赝化电子数量不同进行区分。显而易见地，赝化电子数量越多，则计算量越小，但计算结果的精确程度可能更低。
-## Section 2:
-<PP_MESH>
+Section 2:
+ <PP_MESH>
<PP_R type="real" size=" 602" columns="8">
0.0000 0.0100 0.0200 0.0300 0.0400 0.0500 0.0600 0.0700
<!-- omitted information here -->
@@ -907,8 +907,8 @@ </PP_MESH>
这部分开始出现了关于实空间格点相关量的定义。在 tag 中不仅指定数据类型为实数，也指定当前数据的长度（size），以及数据存储的列数（columns = 8）。PP_R 为格点坐标，PP_RAB 则为格点间距。
-## Section 3:
-<PP_LOCAL type="real" size=" 602" columns="4">
+Section 3:
+ <PP_LOCAL type="real" size=" 602" columns="4">
-4.5793174225E+01 -4.5788454271E+01 -4.5774276797E+01 -4.5750659428E+01
<!-- omitted information here -->
-3.6912752197E+00 -3.6850921941E+00 -3.6789298138E+00 -3.6727880140E+00
@@ -917,8 +917,8 @@ <PP_LOCAL>
部分开始，正式开始写入赝势的具体数值，建立在 <PP_R> 和 <PP_RAB> 所描述的实空间格点上。。<PP_LOCAL> 正是赝势的局域势部分。
-## Section 4:
-<PP_NONLOCAL>
+Section 4:
+ <PP_NONLOCAL>
<PP_BETA.1
type="real"
size=" 602"
@@ -938,8 +938,8 @@ cutoff_radius_index
=" 246" cutoff_radius=" 2.4500000000E+00" >
<!-- omitted information here -->
</PP_BETA.2>
- <PP_BETA.3 type="real" size=" 602" columns="4" index="3" angular_momentum="1"<strong>
-</strong> cutoff_radius_index=" 246" cutoff_radius=" 2.4500000000E+00" >
+ <PP_BETA.3 type="real" size=" 602" columns="4" index="3" angular_momentum="1"
+ cutoff_radius_index=" 246" cutoff_radius=" 2.4500000000E+00" >
<!-- omitted information here -->
</PP_BETA.3>
<PP_BETA.4 type="real" size=" 602" columns="4" index="4" angular_momentum="1"
@@ -956,7 +956,7 @@ \hat{V}^\text{NL}=\sum_{ij}{|\beta_i\rangle D_{ij}\langle\beta_j|}。其中一般被称为非局域势投影子（projector）。
-## Section 5: and
+Section 5: and
<PP_PSWFC>
</PP_PSWFC>
<PP_RHOATOM type="real" size=" 602" columns="4">
@@ -975,7 +975,7 @@ |\beta\rangle和 pswfc 已经乘径向坐标。
-# UnitCell::read_cell_pseudopots()
+UnitCell::read_cell_pseudopots()
link to Github -> link
void UnitCell::read_cell_pseudopots(const std::string &pp_dir, std::ofstream &log)
{
@@ -1030,7 +1030,7 @@ while (ifs.good())
+ while (ifs.good())
{
ifs >> dummy;
if(dummy=="<PP_HEADER>")
@@ -1044,7 +1044,7 @@ if ( ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_MESH>") )
+ if ( ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_MESH>") )
{
read_pseudo_mesh(ifs);
ModuleBase::GlobalFunc::SCAN_END(ifs, "</PP_MESH>");
@@ -1052,7 +1052,7 @@ if (this->nlcc)
+ if (this->nlcc)
{
ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_NLCC>");
read_pseudo_nlcc(ifs);
@@ -1061,12 +1061,12 @@ ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_LOCAL>");
+ ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_LOCAL>");
read_pseudo_local(ifs);
ModuleBase::GlobalFunc::SCAN_END(ifs, "</PP_LOCAL>");
与 类似的还有 , , , 从 则可以读取旋轨耦合相关信息：
-if (has_so)
+ if (has_so)
{
ModuleBase::GlobalFunc::SCAN_BEGIN (ifs,"<PP_ADDINFO>");
read_pseudo_so (ifs);
@@ -1140,7 +1140,7 @@ if(error==0)
+ if(error==0)
{
if(this->atoms[i].flag_empty_element) upf.set_empty_element();
error_ap = upf.average_p(GlobalV::soc_lambda);
@@ -1148,7 +1148,7 @@ if(GlobalV::MY_RANK==0)
+ if(GlobalV::MY_RANK==0)
{
atoms[i].ncpp.set_pseudo_nc( upf );
....
@@ -1178,7 +1178,7 @@ }
该函数属于类 pseudo_nc，而 pseudo_nc 对象为 atom 的数据成员，atoms 则为 UnitCell 的数据成员。pseudo_nc::set_pseudo_h()，pseudo_nc::set_pseudo_atom 和 pseudo_nc::set_pseudo_vl 的内容在此省略，但其分别为将 Hamilton, 原子性质和 Vlocal 相关数据从 upf 对象拷贝。之后(1)使用 lll 刷新为 upf 对象的 projectors 的角动量，然后计算出磁角动量区分时的 projector 个数。(2)取所有 projector 衰减到 0 时候的最大最普适半径。
-# 赝势信息后处理
+赝势信息后处理
回到 module_cell/unitcell.cpp line 663，接下来为每个原子创建目录，在目录中写 [原子label].NONLOCAL 文件。[label].NONLOCAL 文件中内容包含 <HEADER>, <DIJ> 和 <PP_BETA> 三个 tag。
<HEADER> 中包含内容：
ofs << "<HEADER>" << std::endl;
@@ -1222,21 +1222,61 @@ }
ofs << "</PP_BETA>" << std::endl;
-# 赝势信息分发：UnitCell::bcast_unitcell2(void)
+赝势信息分发：UnitCell::bcast_unitcell2(void)
#ifdef __MPI
+接下来对赝势信息进行MPI进程（processor）间的分发：
+#ifdef __MPI
+ bcast_unitcell2();
+#endif
+
+// module_cell/unitcell.cpp:bcast_unitcell2()
+void UnitCell::bcast_unitcell2(void)
+{
+ for (int i = 0; i < ntype; i++)
+ {
+ atoms[i].bcast_atom2();
+ }
+ return;
+}
+
+// module_cell/atom_spec.cpp:Atom::bcast_atom2()
+void Atom::bcast_atom2()
+{
+ this->ncpp.bcast_atom_pseudo();
+}
+
+// module_cell/atom_pseudo.cpp::Atom_pseudo::bcast_atom_pseudo()
+void Atom_pseudo::bcast_atom_pseudo(void)
+{
+....
+ Parallel_Common::bcast_int( lmax );
+....
+ Parallel_Common::bcast_double( etotps );
+....
+ Parallel_Common::bcast_bool( tvanp );
+....
+ Parallel_Common::bcast_string( psd );
+....
+ // below two 'bcast_double' lines of codes seem to have bugs,
+ // on some computers, the code will stuck here for ever.
+ // mohan note 2021-04-28
+ Parallel_Common::bcast_double( dion.c , nbeta * nbeta);
+ Parallel_Common::bcast_double( betar.c, nr * nc );
+}
+
#endif
-# 赝势信息核对
+赝势信息核对
接下来跨原子种类检验泛函是否一致：
-for(int it=0; it<ntype; it++)
+ for(int it=0; it<ntype; it++)
{
if(atoms[0].ncpp.xc_func !=atoms[it].ncpp.xc_func)
{
-# STRU 结构检查：UnitCell::check_structure()
+STRU 结构检查：UnitCell::check_structure()
检验结构中任意两原子之间距离是否大于其固定倍数（<1）的共价半径和，
-check_structure(GlobalV::MIN_DIST_COEF);
+ check_structure(GlobalV::MIN_DIST_COEF);
-# 计算轨道数：UnitCell::cal_natomwfc()
+计算轨道数：UnitCell::cal_natomwfc()
UnitCell::cal_natomwfc() 函数计算所有种类的原子轨道数量加和，对于非 nspin=4，即非 soc（自旋轨道耦合）情况，角量子数 l 和 s 非耦合，l 单独可以作为好的量子数来区分量子态，因此对于每个赝势中定义的 wfc，若其对应 occupation 大于等于 0（即有效 wfc），则对应于其角量子数 l，轨道数量增加 2l+1，即计数其磁量子数 m，也相当于对 alpha 和 beta spin 的单独计数。对于 nspin=4 的情况，若考虑 soc，则轨道数对 j=l+s 的情况，当前原子种类当前角量子数对应轨道数量记为 2l+1+1，否则为 2l+1。对于非 soc 但 nspin=4，当前原子种类轨道当前角量子数对应轨道数量记(2l+1)*2：
void UnitCell::cal_natomwfc(std::ofstream &log)
{
@@ -1291,9 +1331,9 @@ 计算跨原子种类最大角量子数 UnitCell::lmax 和某 l 对应最大 zeta 数 UnitCell::nmax，以及跨原子种类的类内 zeta 数总和最大值 UnitCell::nmax_total
寻找赝势中最大角量子数 UnitCell::lmax_ppwf。
-# 价电子数核对
+价电子数核对
核对赝势中定义的价电子数与 ABACUS 预置库中原子的最小价电子数
-# 获取最大格点数量：UnitCell::cal_meshx()
+获取最大格点数量：UnitCell::cal_meshx()
计算跨原子种类的最大格点数量，存储在 UnitCell::meshx 中，目前 ABACUS 代码中变量命名后缀 x 可能代表 max，正如之前看到 npwx 等。
至此，我们离开函数 UnitCell::read_pseudo()，回到 ModuleESolver::ESolver_FP::Init() 函数。
@@ -1304,7 +1344,7 @@ Introduction to ABACUS: Path to PW calculation - Part 2
下篇：Introduction to ABACUS: Path to PW calculation - Part 4
@@ -1348,7 +1388,7 @@ No results matching "
var gitbook = gitbook || [];
gitbook.push(function() {
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example","attributes":{},"skip":false,"key":"1.2.10.5"}]},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"develop-path3.md","mtime":"2023-10-04T15:11:45.401Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-10-04T15:29:41.868Z"},"basePath":".","book":{"language":""}});
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diff --git a/_book/develop-path4.html b/_book/develop-path4.html
index 1840948c..2b9cddf9 100644
--- a/_book/develop-path4.html
+++ b/_book/develop-path4.html
@@ -750,14 +750,14 @@ Driver
-Driver::atomic_world()
-Driver::driver_run()
-多层继承：Init() functions in esolver class
-Trigger: ESolver_FP::Init()
-平面波格点初始化：PW_Basis:: initgrids()
+Driver
+Driver::atomic_world()
+Driver::driver_run()
+多层继承：Init() functions in esolver class
+Trigger: ESolver_FP::Init()
+平面波格点初始化：PW_Basis:: initgrids()
完成了 INPUT 和 STRU，以及赝势文件的读取环节，接下来我们来到平面波的初始化设置相关部分。
-void ESolver_FP::Init(Input& inp, UnitCell& cell)
+ void ESolver_FP::Init(Input& inp, UnitCell& cell)
{
....
if (inp.nx * inp.ny * inp.nz == 0)
@@ -782,7 +782,7 @@ virtual void initgrids(const double lat0_in,const ModuleBase::Matrix3 latvec_in,
+ virtual void initgrids(const double lat0_in,const ModuleBase::Matrix3 latvec_in,
const double gridecut)
{
// generation of nx, ny and nz are omitted here
@@ -868,7 +868,7 @@ }
❗ 注意：这里还完成了倒空间格点数量 fftnx, fftny 和 fftnz 的赋值。因为 FFT 变换前后的格点数量一般相同，因此 fftnx = nx，fftny = ny，...。
-
+图 1. 然后对平面波在 MPI 进程间进行分发：
//module_esolver/esolver_fp.cpp
void ESolver_FP::Init(Input& inp, UnitCell& cell)
@@ -889,9 +889,9 @@ ::
timer::tick(this->classname, "setuptransform");
}
-PW_Basis::setuptransform()（link）
-# 并行机制简述
-## 并行池
+PW_Basis::setuptransform()（link）
+并行机制简述
+并行池
到这里，我们不得不开始对平面波的 MPI 并行机制有一个大致的认识。在 ABACUS 中，CPU（=processor）首先根据不同的布里渊区 k 点分组被划分成不同的并行池（parallelizaiton pool），每个 pool 都包含几个 k 点，在每个 pool 里面会有完整的对该 k 点求解 Kohn-Sham 方程的过程。因此，在每个 pool 中采用一定数量的 CPU 进程来完成计算。在 INPUT 文件中，KPAR 参数决定了并行池的数量（即 pool 的个数）。换句话说，ABACUS 的 k 点并行机制为，将 k 点（设其数量为 nkpt）分配在 KPAR 个 pool 中，若一共有 nproc 个 processor，则：
- 每个 pool 有
nproc/KPAR 个 processor
@@ -899,7 +899,7 @@ ## MPI 进程编号：rank
+MPI 进程编号：rank
rank 是一个在 MPI 并行里常被用到的变量。在拥有不止一个 processor 的时候，每个 processor 都具有唯一的编号，称为 rank。如果在每个 processor 都有 rank 的基础上还定义了 pool，以及在每个 pool 中的 processor 数量，则 processor 除了有跨 pool 的全局 rank，也可以有 pool 之内的局部 rank，这部分内容见 module_base/global_variable.cpp:
int NPROC = 1;
int KPAR = 1;
@@ -926,7 +926,7 @@ }
}
-## 并行策略
+并行策略
于是问题便到来：在并行条件下，代码究竟是如何执行的？
- 对于多核 CPU，是否运行在其上的所有程序都进行了并行化？
@@ -950,9 +950,9 @@ ## OpenMP-MPI 混合编程
+OpenMP-MPI 混合编程
通常来讲，尽管 OpenMP 提供了线程并行，但由于共享内存可能并不存在于 processors 之间，或 computer, nodes 之间，且没有适合的内存共享系统（multi-socket server），此时如果以 OpenMP 放心运行，则可能得出错误结果或直接报错——因为内存无法访问。对于这种情况，需要使用 MPI（Message passing interface）来维持无内存共享处理单元之间的信息交换，以及信息分发和分布计算，而在处理单元内部，即可以共享内存的域内，则可以通过 OpenMP 技术来进行线程级并行。
-# 实空间格点分发
+实空间格点分发
在简单介绍完并行机制后，我们知道，对于未显式以并行方式实现的函数，其运行将在每一个 processor。在接下来的平面波分发过程中，请始终牢记这一理念，尤其在 processor-local 变量和 processor-global 变量的传值过程中。
稍加回溯：
void ESolver_FP::Init(Input& inp, UnitCell& cell)
@@ -968,7 +968,7 @@ ## 实空间：PW_Basis::distribute_r()
+实空间：PW_Basis::distribute_r()
❗Attention
注意，此时实际调用的也是 PW_Basis_Big 而非 PW_Basis 的 distribute_r() 函数。
@@ -1011,8 +1011,8 @@ {
....
该判断不会 always true。因此 PW_Basis::distribute_r() 将 3D 实空间格点，按照 z 方向进行分发，分给了不同的 processors，并赋值 this->npz，this->nplane, this->startz_current 和 this->nrxx，意义分别为当前 processor 的 z 方向格点数量、xy 平面数量、z 格点的起始索引以及当前 processor 所分得实空间格点总数（分配后 z 方向格点 ×xy 平面格点）。
-
-## 倒空间：PW_Basis::distribute_g()
+图 2. PW_Basis::distribute_r()：设一个pool中有5个processors 倒空间：PW_Basis::distribute_g()
倒空间格点的分发采用了和实空间不同的方式，这主要是因为倒空间“球”的存在（ecutwfc 和 ecutrho），使得非空间中所有点都需要考虑在内，而实空间则并非如此。更一般而言，有限的实空间带来无限的倒空间（即实空间 delta 函数需要无限数量的平面波展开）延展，而有限的倒空间（倒空间 delta 点）带来无限的实空间延展（如一个平面波）。
🔧重构信息
@@ -1066,7 +1066,7 @@
delete
[] st_bottom2D; delete[] st_length2D;
}
-### 分发最小单元：“棍子” - 准备工作
+分发最小单元：“棍子” - 准备工作
穿过布里渊区的整数点（2pi/a 的整数倍）都代表一个三个 index 的平面波，而一系列的点在截断半径以内沿着某个方向就组成了所谓的“stick”（代表平面波集合的“棍子”，一个“棍子”包含了多个平面波，简称就叫“棍子”）。
PW_Basis::count_pw_st() 函数（Link）计算了每个(x,y)对应的“棍子”的底部和“长度”，即对倒空间只分辨(x,y)，则会得到沿 z 方向的点的集合，被称为“棍子”。而“棍子”区域内部每一个点都代表一个平面波。“棍子”的底部对应于最小的 iz 值，“根子”的长度则为当前(x,y)所包含的平面波数量：
for (int ix = ix_start; ix <= ix_end; ++ix)
@@ -1098,7 +1098,7 @@ }
}
-
+图 3. this->count_pw_st(st_length2D, st_bottom2D) 在倒空间分发平面波时，由于 x/y/z 均等在正负半轴 span，因此常常会涉及到 C++ 不支持负数索引的问题（btw: Python 和 FORTRAN 支持负数索引，但支持方式不同），ABACUS 当前所采取的策略是：
if (x<0) x += this->nx; if (y<0) y += this->ny; if (z<0) z += this->nz;
@@ -1107,7 +1107,7 @@ ### “棍子”的分发和分发记录
+“棍子”的分发和分发记录
PW_Basis::collect_st() 和 PW_Basis::divide_sticks_1() 分别排序与分发“棍子”到不同 processor：
- 按照棍子从长到短顺序进行排序，即
st_length2D 由大到小排序，然后适用于 st_bottom2D 等变量
@@ -1136,7 +1136,7 @@ this
->nstnz = this->nst * this->nz;
....
-### 映射表：OOP？
+映射表：OOP？
在倒空间平面波的分发过程中，共建立过四个映射表，分别是 this->fftixy2ip, this->istot2ixy, this->ig2isz 和 this->is2fftixy，其意义分别为：
No results matching "
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diff --git a/_book/develop-path1.html b/_book/develop-path1.html
index 1de92b86..d41c1be3 100644
--- a/_book/develop-path1.html
+++ b/_book/develop-path1.html
@@ -1112,8 +1112,8 @@ <
Input_Conv::Convert()
这个函数实现了从 Input 类对象的数据成员到 GlobalV 和 GlobalC 等全局变量集合的转换。相当于从 Input 到 GlobalV 和 GlobalC，以及其他直接的类的参数上载：
-其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
+其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
void Input_Conv::Convert(void)
{
....
@@ -1308,7 +1308,7 @@
不要忘记我们已经完成 Driver::reading() 函数内容，到达 Driver::atomic_world()。这一点从本文档设置的分级目录中也可以看得到。
-cppvoid Driver::init()
+void Driver::init()
{
this->reading();
this->atomic_world(); // <- here!
@@ -1518,7 +1518,7 @@ 从 SIAB 到 ABACUS（一）：准备工作（施工中 🚧）
下篇：Introduction to ABACUS: Path to PW calculation - Part 2
@@ -1562,7 +1562,7 @@ No results matching "
var gitbook = gitbook || [];
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V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","attributes":{},"skip":false,"key":"1.1.15.5"},{"backlink":"abacus-surface6.html#fig1.1.16.1","level":"1.1.16","list_caption":"Figure: 一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","alt":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","nro":14,"url":"picture/fig_surface6-1.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","attributes":{},"skip":false,"key":"1.1.16.1"},{"backlink":"abacus-surface6.html#fig1.1.16.2","level":"1.1.16","list_caption":"Figure: 静电势（Electrostatic Potential）沿超胞Z轴变化图","alt":"静电势（Electrostatic Potential）沿超胞Z轴变化图","nro":15,"url":"picture/fig_surface6-2.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"静电势（Electrostatic Potential）沿超胞Z轴变化图","attributes":{},"skip":false,"key":"1.1.16.2"},{"backlink":"develop-path4.html#fig1.2.9.1","level":"1.2.9","list_caption":"Figure: ","alt":" 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1)","alt":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","nro":21,"url":"picture/fig_path5-11.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","attributes":{},"skip":false,"key":"1.2.10.3"},{"backlink":"develop-path5.html#fig1.2.10.4","level":"1.2.10","list_caption":"Figure: 1-dimensional example","alt":"1-dimensional example","nro":22,"url":"picture/fig_path5-12.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"1-dimensional example","attributes":{},"skip":false,"key":"1.2.10.4"},{"backlink":"develop-path5.html#fig1.2.10.5","level":"1.2.10","list_caption":"Figure: 2-dimensional example","alt":"2-dimensional example","nro":23,"url":"picture/fig_path5-13.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"2-dimensional example","attributes":{},"skip":false,"key":"1.2.10.5"}]},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"develop-path1.md","mtime":"2023-10-04T14:18:52.079Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-10-04T15:29:41.868Z"},"basePath":".","book":{"language":""}});
});
diff --git a/_book/develop-path2.html b/_book/develop-path2.html
index 191dfe74..d829579b 100644
--- a/_book/develop-path2.html
+++ b/_book/develop-path2.html
@@ -1028,7 +1028,7 @@ // a(i) is lattice vector
}
-我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
+我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
UnitCell::read_atom_positions()
🔧重构思考
@@ -1042,7 +1042,7 @@
::
GlobalFunc::READ_VALUE( ifpos, Coordinate);
STRU 第二行指定坐标类型，被读取为 UnitCell::Coordinate。UnitCell::Coordinate 在 STRU 里有不同选项，⚙ 决定原子的具体位置和单位：
-if(Coordinate != "Cartesian"
+ if(Coordinate != "Cartesian"
&& Coordinate != "Direct"
&& Coordinate != "Cartesian_angstrom"
&& Coordinate != "Cartesian_au"
@@ -1092,7 +1092,7 @@ int na = 0;
+ int na = 0;
this->nat = 0;
assert(ntype>0);
for (int it = 0;it < ntype; it++)
@@ -1105,7 +1105,7 @@ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
bool sequence_match = false;
for(int it2=0; it2<ntype; it2++)
{
@@ -1121,7 +1121,7 @@ }
读取当前原子类型的 starting_magnetization、原子总数 na
-ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
...
ModuleBase::GlobalFunc::READ_VALUE(ifpos, na);
this->atoms[it].na = na;
@@ -1149,17 +1149,17 @@ [
it].m_loc_ = new ModuleBase::Vector3<double>[na];
⚙ 然后在 ATOMIC_POSITIONS 中读取：
-atoms[it].mass = this->atom_mass[it];
+ atoms[it].mass = this->atom_mass[it];
❗ 此处的 atoms[it].mass 与 this->atom_mass[it] 的用法与 atomis[it].label 与 this->atom_label[it] 不同：传值 vs 核对。
接下来读取类中每个原子的速度信息，在做分子动力学模拟的时候可能需要用到：
-for (int ia = 0;ia < na; ia++)
+ for (int ia = 0;ia < na; ia++)
{
ifpos >> v.x >> v.y >> v.z;
然而，当前 STRU 文件在 ATOMIC_POSITIONS 的设计比较复杂，其可以包括任何一组 atom-specific 数据，且数量和顺序均不受限制，这导致判断条件变得复杂，详见 module_cell/read_atoms.cpp:line 536 - 567（link）。
atoms[it].mag 的赋值并非直接读取：
-else if ( tmpid == "mag" || tmpid == "magmom")
+ else if ( tmpid == "mag" || tmpid == "magmom")
{
set_element_mag_zero = true;
double tmpamg=0; ifpos >> tmpamg;
@@ -1185,7 +1185,7 @@ }
⚙ 若 mag/magmom 后有一个值，则读取其值赋给 atoms[it]::mag[ia]，将 input_vec_mag 置为 false，若有三个值，则三个值依次被传入 atoms[it].m_loc_[ia].x, atoms[it].m_loc_[ia].y 和 atoms[it].m_loc_[ia].z，并将 input_vec_mag 置为 true，之后其向量模长为 atoms[it]::mag[ia]，然后在使用 angle1, angle2 来重新生成 mag。
-if(GlobalV::NSPIN==4)
+ if(GlobalV::NSPIN==4)
{
if(GlobalV::NONCOLIN)
{
@@ -1227,7 +1227,7 @@ pw.x input description
ABACUS 对 nspin=4 情况的参数处理：
//module_io/input_conv.cpp line 376
if (INPUT.noncolin || INPUT.lspinorb)
@@ -1312,7 +1312,7 @@
UnitCell::setup_cell(): the rest, and an example of backtracking unclear variable
离开 STRU 文件的解析部分，接下来计算了初始磁化强度：
-//after read STRU, calculate initial total magnetization when NSPIN=2
+ //after read STRU, calculate initial total magnetization when NSPIN=2
if(GlobalV::NSPIN == 2 && !GlobalV::TWO_EFERMI)
{
for(int it = 0;it<this->ntype; it++)
@@ -1326,31 +1326,25 @@ if (std::abs(INPUT.nupdown) > 1e-6)
- {
- GlobalV::TWO_EFERMI = true;
- GlobalV::nupdown = INPUT.nupdown;
- }
-
-因此 GlobalV::TWO_EFERMI 变量实际依赖于 INPUT.nupdown。
-
-- 接下来在
module_io/input.cpp 中寻找含 INPUT.nupdown 的 if(strcmp(...)) 单元，查看在 INPUT 文件中是何参数赋予其具体值：
-
-else if (strcmp("nupdown", word) == 0)
+在 module_io/input_conv.cpp 中寻找该变量，是何变量赋其值，发现： if (std::abs(INPUT.nupdown) > 1e-6)
{
- read_value(ifs, nupdown);
- }
+ GlobalV::TWO_EFERMI = true;
+ GlobalV::nupdown = INPUT.nupdown;
+ }
-即 INPUT.nupdown 在 INPUT 中也为 nupdown。接下来打开 Full keyword list 寻找其解释。
-
+ 因此 GlobalV::TWO_EFERMI 变量实际依赖于 INPUT.nupdown。
+接下来在 module_io/input.cpp 中寻找含 INPUT.nupdown 的 if(strcmp(...)) 单元，查看在 INPUT 文件中是何参数赋予其具体值： else if (strcmp("nupdown", word) == 0)
+ {
+ read_value(ifs, nupdown);
+ }
+
+即 INPUT.nupdown 在 INPUT 中也为 nupdown。接下来打开 Full keyword list 寻找其解释。
得到结果，即 nupdown 为 spin up 和 spin down 电子数量差值：
因此该部分逻辑为：若未使用 nupdown 来指定单电子数量，则对每种原子内每个原子，累加其 mag/magmom，即磁矩模长，赋予 GlobalV::nupdown。❗ 但对于两种方式均赋予，但值不一致的情况未进行处理。
接下来根据在 STRU 中读取的晶胞参数，计算晶胞体积，并计算倒空间矢量（在上篇中已经对 latvec, G, GT, GGT 有所介绍，invGGT 的意义也不言自明）：
-this->omega = std::abs( latvec.Det() ) * this->lat0 * lat0 * lat0 ;
+ this->omega = std::abs( latvec.Det() ) * this->lat0 * lat0 * lat0 ;
this->GT = latvec.Inverse();
this->G = GT.Transpose();
@@ -1442,7 +1436,7 @@ =
static_cast<ModulePW::PW_Basis_Big*>(pw_rho);
对于 ESolver 本身，其指针对象 p_esolver 实际上也有类似操作：
-//Some API to operate E_Solver
+ //Some API to operate E_Solver
void init_esolver(ESolver*& p_esolver)
{
//determine type of esolver based on INPUT information
@@ -1907,7 +1901,7 @@ Introduction to ABACUS: Path to PW calculation - Part 1
下篇：Introduction to ABACUS: Path to PW calculation - Part 3
@@ -1951,7 +1945,7 @@ No results matching "
var gitbook = gitbook || [];
gitbook.push(function() {
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采用PBE交换关联泛函和自旋极化得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出不加电场时，两个自旋方向的能带图几乎一样，都有带隙。","alt":"采用PBE交换关联泛函和自旋极化得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出不加电场时，两个自旋方向的能带图几乎一样，都有带隙。","nro":12,"url":"picture/fig_surface5-4.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"采用PBE交换关联泛函和自旋极化得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出不加电场时，两个自旋方向的能带图几乎一样，都有带隙。","attributes":{},"skip":false,"key":"1.1.15.4"},{"backlink":"abacus-surface5.html#fig1.1.15.5","level":"1.1.15","list_caption":"Figure: 采用PBE交换关联泛函和自旋极化，再给体系加上0.1 V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","alt":"采用PBE交换关联泛函和自旋极化，再给体系加上0.1 V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","nro":13,"url":"picture/fig_surface5-5.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"采用PBE交换关联泛函和自旋极化，再给体系加上0.1 V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","attributes":{},"skip":false,"key":"1.1.15.5"},{"backlink":"abacus-surface6.html#fig1.1.16.1","level":"1.1.16","list_caption":"Figure: 一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","alt":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","nro":14,"url":"picture/fig_surface6-1.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","attributes":{},"skip":false,"key":"1.1.16.1"},{"backlink":"abacus-surface6.html#fig1.1.16.2","level":"1.1.16","list_caption":"Figure: 静电势（Electrostatic Potential）沿超胞Z轴变化图","alt":"静电势（Electrostatic Potential）沿超胞Z轴变化图","nro":15,"url":"picture/fig_surface6-2.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"静电势（Electrostatic Potential）沿超胞Z轴变化图","attributes":{},"skip":false,"key":"1.1.16.2"},{"backlink":"develop-path4.html#fig1.2.9.1","level":"1.2.9","list_caption":"Figure: ","alt":" ","nro":16,"url":"picture/fig_path4-1.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":" ","attributes":{},"skip":false,"key":"1.2.9.1"},{"backlink":"develop-path4.html#fig1.2.9.2","level":"1.2.9","list_caption":"Figure: PW_Basis::distribute_r()：设一个pool中有5个processors","alt":"PW_Basis::distribute_r()：设一个pool中有5个processors","nro":17,"url":"picture/fig_path4-2.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"PW_Basis::distribute_r()：设一个pool中有5个processors","attributes":{},"skip":false,"key":"1.2.9.2"},{"backlink":"develop-path4.html#fig1.2.9.3","level":"1.2.9","list_caption":"Figure: this->count_pw_st(st_length2D, st_bottom2D)","alt":"this->count_pw_st(st_length2D, st_bottom2D)","nro":18,"url":"picture/fig_path4-3.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"this->count_pw_st(st_length2D, st_bottom2D)","attributes":{},"skip":false,"key":"1.2.9.3"},{"backlink":"develop-path5.html#fig1.2.10.1","level":"1.2.10","list_caption":"Figure: 善用Ctrl+F","alt":"善用Ctrl+F","nro":19,"url":"picture/fig_path5-9.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"善用Ctrl+F","attributes":{},"skip":false,"key":"1.2.10.1"},{"backlink":"develop-path5.html#fig1.2.10.2","level":"1.2.10","list_caption":"Figure: klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","alt":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","nro":20,"url":"picture/fig_path5-10.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","attributes":{},"skip":false,"key":"1.2.10.2"},{"backlink":"develop-path5.html#fig1.2.10.3","level":"1.2.10","list_caption":"Figure: klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","alt":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","nro":21,"url":"picture/fig_path5-11.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","attributes":{},"skip":false,"key":"1.2.10.3"},{"backlink":"develop-path5.html#fig1.2.10.4","level":"1.2.10","list_caption":"Figure: 1-dimensional example","alt":"1-dimensional example","nro":22,"url":"picture/fig_path5-12.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"1-dimensional example","attributes":{},"skip":false,"key":"1.2.10.4"},{"backlink":"develop-path5.html#fig1.2.10.5","level":"1.2.10","list_caption":"Figure: 2-dimensional example","alt":"2-dimensional example","nro":23,"url":"picture/fig_path5-13.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"2-dimensional example","attributes":{},"skip":false,"key":"1.2.10.5"}]},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"develop-path2.md","mtime":"2023-10-04T14:37:12.149Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-10-04T15:29:41.868Z"},"basePath":".","book":{"language":""}});
});
diff --git a/_book/develop-path3.html b/_book/develop-path3.html
index b8de33d9..09176394 100644
--- a/_book/develop-path3.html
+++ b/_book/develop-path3.html
@@ -750,11 +750,11 @@ Driver
-Driver::atomic_world()
-Driver::driver_run()
-多层继承：Init() functions in esolver class
-Trigger: ESolver_FP::Init()
+Driver
+Driver::atomic_world()
+Driver::driver_run()
+多层继承：Init() functions in esolver class
+Trigger: ESolver_FP::Init()
承接上篇中已经导入的结构信息，以及了解到构造函数及其伴随的变量初始化和 ABACUS 里应用到的 C++ 多态编程，接下来即将（逐渐）步入 ABACUS 的核心内容。我们暂时跳过位于 source/driver_run.cpp:driver_run() 的：
// 3. For these two types of calculations
// nothing else need to be initialized
@@ -830,14 +830,14 @@ }
同理，ESolver_KS 的数据成员，也被 ESolver_KS_PW 继承。ESolver_FP::Init() 首先调用 UnitCell::read_pseudo() 函数进行赝势文件读取，而将赝势文件读取任务放在 FP 层级下，也暗示对于 ABACUS 的第一性原理方法实现来讲，都需要使用赝势。
-Pseudopotential import: UnitCell::read_pseudo()
+Pseudopotential import: UnitCell::read_pseudo()
void UnitCell::read_pseudo(std::ofstream &ofs)
{
read_cell_pseudopots(GlobalV::global_pseudo_dir, ofs);
在解读赝势文件读取功能之前，首先需要对赝势文件的结构和信息做一定程度的了解。
-# ONCV pseudopotential file
-## Section 0: Norm-conserving conditions, generation of pseudopotential and header of exact UPF file
+ONCV pseudopotential file
+Section 0: Norm-conserving conditions, generation of pseudopotential and header of exact UPF file
赝势的意义不言自明，其中模守恒赝势需满足如下条件：
- （赝势得到的能级和全电子方法求解的能级一样，这里 ps 代表 pseudopotentials）
@@ -852,7 +852,7 @@ V_l(r)=\frac{1}{\phi^\text{ps}_l(r)}[\epsilon^\text{ps}_l-\frac{\hbar^2}{2m}\frac{l(l+1)}{r^2}+\frac{\hbar^2}{2m}\frac{d^2}{dr^2}]\phi^\text{ps}_l(r)，解得。
- 扣除中 Hartree、xc 部分，得到：。
-更多细节见
+更多细节见：www.tcm.phy.cam.ac.uk
<UPF version="2.0.1">
<PP_INFO>
<!-- omitted information here -->
@@ -865,8 +865,8 @@ <!-- -->
从 UPF 文件（注意 UPF 文件也有不同的版本，目前 ABACUS 都支持，若有不支持的，可以提 Github 的 issues 进行讨论）开始，截止到 <PP_HEADER> 之前，提供了赝势文件的作者信息，引用信息以及生成赝势文件所使用的程序和相应输入文件，并附带输入文件参数中的解释。由于此块内容对实际计算并不起作用，因此暂时略过。
-## Section 1:
-<PP_HEADER
+Section 1:
+ <PP_HEADER
generated="Generated using ONCVPSP code by D. R. Hamann" author="Martin Schlipf and Francois Gygi"
date="150105" comment=""
element="Al"
@@ -890,8 +890,8 @@ number_of_proj
="4"/>
<PP_HEADER> 部分尽管已经位于所谓“not human readable”区域，但也并非如此。这部分“标签”（HTML 语境）/block 实际上包含了众多精简过的信息，如元素名称（element）、赝势类型（pseudo_type，模守恒，norm-conserving，NC），相对论效应（relativistic），是否为超软赝势等等信息。当前 Al 理论上其原子序数 13，因此有 13 个电子，但此处 z_valence 参数为 11，即有两个 1s 电子被赝化，只留下 2s, 2p, 3s, 3p 电子共 2+6+2+1 个。对于某些元素，甚至有大核赝势与小核赝势之分，根据赝化电子数量不同进行区分。显而易见地，赝化电子数量越多，则计算量越小，但计算结果的精确程度可能更低。
-## Section 2:
-<PP_MESH>
+Section 2:
+ <PP_MESH>
<PP_R type="real" size=" 602" columns="8">
0.0000 0.0100 0.0200 0.0300 0.0400 0.0500 0.0600 0.0700
<!-- omitted information here -->
@@ -907,8 +907,8 @@ </PP_MESH>
这部分开始出现了关于实空间格点相关量的定义。在 tag 中不仅指定数据类型为实数，也指定当前数据的长度（size），以及数据存储的列数（columns = 8）。PP_R 为格点坐标，PP_RAB 则为格点间距。
-## Section 3:
-<PP_LOCAL type="real" size=" 602" columns="4">
+Section 3:
+ <PP_LOCAL type="real" size=" 602" columns="4">
-4.5793174225E+01 -4.5788454271E+01 -4.5774276797E+01 -4.5750659428E+01
<!-- omitted information here -->
-3.6912752197E+00 -3.6850921941E+00 -3.6789298138E+00 -3.6727880140E+00
@@ -917,8 +917,8 @@ <PP_LOCAL>
部分开始，正式开始写入赝势的具体数值，建立在 <PP_R> 和 <PP_RAB> 所描述的实空间格点上。。<PP_LOCAL> 正是赝势的局域势部分。
-## Section 4:
-<PP_NONLOCAL>
+Section 4:
+ <PP_NONLOCAL>
<PP_BETA.1
type="real"
size=" 602"
@@ -938,8 +938,8 @@ cutoff_radius_index
=" 246" cutoff_radius=" 2.4500000000E+00" >
<!-- omitted information here -->
</PP_BETA.2>
- <PP_BETA.3 type="real" size=" 602" columns="4" index="3" angular_momentum="1"<strong>
-</strong> cutoff_radius_index=" 246" cutoff_radius=" 2.4500000000E+00" >
+ <PP_BETA.3 type="real" size=" 602" columns="4" index="3" angular_momentum="1"
+ cutoff_radius_index=" 246" cutoff_radius=" 2.4500000000E+00" >
<!-- omitted information here -->
</PP_BETA.3>
<PP_BETA.4 type="real" size=" 602" columns="4" index="4" angular_momentum="1"
@@ -956,7 +956,7 @@ \hat{V}^\text{NL}=\sum_{ij}{|\beta_i\rangle D_{ij}\langle\beta_j|}。其中一般被称为非局域势投影子（projector）。
-## Section 5: and
+Section 5: and
<PP_PSWFC>
</PP_PSWFC>
<PP_RHOATOM type="real" size=" 602" columns="4">
@@ -975,7 +975,7 @@ |\beta\rangle和 pswfc 已经乘径向坐标。
-# UnitCell::read_cell_pseudopots()
+UnitCell::read_cell_pseudopots()
link to Github -> link
void UnitCell::read_cell_pseudopots(const std::string &pp_dir, std::ofstream &log)
{
@@ -1030,7 +1030,7 @@ while (ifs.good())
+ while (ifs.good())
{
ifs >> dummy;
if(dummy=="<PP_HEADER>")
@@ -1044,7 +1044,7 @@ if ( ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_MESH>") )
+ if ( ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_MESH>") )
{
read_pseudo_mesh(ifs);
ModuleBase::GlobalFunc::SCAN_END(ifs, "</PP_MESH>");
@@ -1052,7 +1052,7 @@ if (this->nlcc)
+ if (this->nlcc)
{
ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_NLCC>");
read_pseudo_nlcc(ifs);
@@ -1061,12 +1061,12 @@ ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_LOCAL>");
+ ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_LOCAL>");
read_pseudo_local(ifs);
ModuleBase::GlobalFunc::SCAN_END(ifs, "</PP_LOCAL>");
与 类似的还有 , , , 从 则可以读取旋轨耦合相关信息：
-if (has_so)
+ if (has_so)
{
ModuleBase::GlobalFunc::SCAN_BEGIN (ifs,"<PP_ADDINFO>");
read_pseudo_so (ifs);
@@ -1140,7 +1140,7 @@ if(error==0)
+ if(error==0)
{
if(this->atoms[i].flag_empty_element) upf.set_empty_element();
error_ap = upf.average_p(GlobalV::soc_lambda);
@@ -1148,7 +1148,7 @@ if(GlobalV::MY_RANK==0)
+ if(GlobalV::MY_RANK==0)
{
atoms[i].ncpp.set_pseudo_nc( upf );
....
@@ -1178,7 +1178,7 @@ }
该函数属于类 pseudo_nc，而 pseudo_nc 对象为 atom 的数据成员，atoms 则为 UnitCell 的数据成员。pseudo_nc::set_pseudo_h()，pseudo_nc::set_pseudo_atom 和 pseudo_nc::set_pseudo_vl 的内容在此省略，但其分别为将 Hamilton, 原子性质和 Vlocal 相关数据从 upf 对象拷贝。之后(1)使用 lll 刷新为 upf 对象的 projectors 的角动量，然后计算出磁角动量区分时的 projector 个数。(2)取所有 projector 衰减到 0 时候的最大最普适半径。
-# 赝势信息后处理
+赝势信息后处理
回到 module_cell/unitcell.cpp line 663，接下来为每个原子创建目录，在目录中写 [原子label].NONLOCAL 文件。[label].NONLOCAL 文件中内容包含 <HEADER>, <DIJ> 和 <PP_BETA> 三个 tag。
<HEADER> 中包含内容：
ofs << "<HEADER>" << std::endl;
@@ -1222,21 +1222,61 @@ }
ofs << "</PP_BETA>" << std::endl;
-# 赝势信息分发：UnitCell::bcast_unitcell2(void)
+赝势信息分发：UnitCell::bcast_unitcell2(void)
#ifdef __MPI
+接下来对赝势信息进行MPI进程（processor）间的分发：
+#ifdef __MPI
+ bcast_unitcell2();
+#endif
+
+// module_cell/unitcell.cpp:bcast_unitcell2()
+void UnitCell::bcast_unitcell2(void)
+{
+ for (int i = 0; i < ntype; i++)
+ {
+ atoms[i].bcast_atom2();
+ }
+ return;
+}
+
+// module_cell/atom_spec.cpp:Atom::bcast_atom2()
+void Atom::bcast_atom2()
+{
+ this->ncpp.bcast_atom_pseudo();
+}
+
+// module_cell/atom_pseudo.cpp::Atom_pseudo::bcast_atom_pseudo()
+void Atom_pseudo::bcast_atom_pseudo(void)
+{
+....
+ Parallel_Common::bcast_int( lmax );
+....
+ Parallel_Common::bcast_double( etotps );
+....
+ Parallel_Common::bcast_bool( tvanp );
+....
+ Parallel_Common::bcast_string( psd );
+....
+ // below two 'bcast_double' lines of codes seem to have bugs,
+ // on some computers, the code will stuck here for ever.
+ // mohan note 2021-04-28
+ Parallel_Common::bcast_double( dion.c , nbeta * nbeta);
+ Parallel_Common::bcast_double( betar.c, nr * nc );
+}
+
#endif
-# 赝势信息核对
+赝势信息核对
接下来跨原子种类检验泛函是否一致：
-for(int it=0; it<ntype; it++)
+ for(int it=0; it<ntype; it++)
{
if(atoms[0].ncpp.xc_func !=atoms[it].ncpp.xc_func)
{
-# STRU 结构检查：UnitCell::check_structure()
+STRU 结构检查：UnitCell::check_structure()
检验结构中任意两原子之间距离是否大于其固定倍数（<1）的共价半径和，
-check_structure(GlobalV::MIN_DIST_COEF);
+ check_structure(GlobalV::MIN_DIST_COEF);
-# 计算轨道数：UnitCell::cal_natomwfc()
+计算轨道数：UnitCell::cal_natomwfc()
UnitCell::cal_natomwfc() 函数计算所有种类的原子轨道数量加和，对于非 nspin=4，即非 soc（自旋轨道耦合）情况，角量子数 l 和 s 非耦合，l 单独可以作为好的量子数来区分量子态，因此对于每个赝势中定义的 wfc，若其对应 occupation 大于等于 0（即有效 wfc），则对应于其角量子数 l，轨道数量增加 2l+1，即计数其磁量子数 m，也相当于对 alpha 和 beta spin 的单独计数。对于 nspin=4 的情况，若考虑 soc，则轨道数对 j=l+s 的情况，当前原子种类当前角量子数对应轨道数量记为 2l+1+1，否则为 2l+1。对于非 soc 但 nspin=4，当前原子种类轨道当前角量子数对应轨道数量记(2l+1)*2：
void UnitCell::cal_natomwfc(std::ofstream &log)
{
@@ -1291,9 +1331,9 @@ 计算跨原子种类最大角量子数 UnitCell::lmax 和某 l 对应最大 zeta 数 UnitCell::nmax，以及跨原子种类的类内 zeta 数总和最大值 UnitCell::nmax_total
寻找赝势中最大角量子数 UnitCell::lmax_ppwf。
-# 价电子数核对
+价电子数核对
核对赝势中定义的价电子数与 ABACUS 预置库中原子的最小价电子数
-# 获取最大格点数量：UnitCell::cal_meshx()
+获取最大格点数量：UnitCell::cal_meshx()
计算跨原子种类的最大格点数量，存储在 UnitCell::meshx 中，目前 ABACUS 代码中变量命名后缀 x 可能代表 max，正如之前看到 npwx 等。
至此，我们离开函数 UnitCell::read_pseudo()，回到 ModuleESolver::ESolver_FP::Init() 函数。
@@ -1304,7 +1344,7 @@ Introduction to ABACUS: Path to PW calculation - Part 2
下篇：Introduction to ABACUS: Path to PW calculation - Part 4
@@ -1348,7 +1388,7 @@ No results matching "
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采用PBE交换关联泛函和自旋极化得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出不加电场时，两个自旋方向的能带图几乎一样，都有带隙。","alt":"采用PBE交换关联泛函和自旋极化得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出不加电场时，两个自旋方向的能带图几乎一样，都有带隙。","nro":12,"url":"picture/fig_surface5-4.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"采用PBE交换关联泛函和自旋极化得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出不加电场时，两个自旋方向的能带图几乎一样，都有带隙。","attributes":{},"skip":false,"key":"1.1.15.4"},{"backlink":"abacus-surface5.html#fig1.1.15.5","level":"1.1.15","list_caption":"Figure: 采用PBE交换关联泛函和自旋极化，再给体系加上0.1 V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","alt":"采用PBE交换关联泛函和自旋极化，再给体系加上0.1 V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","nro":13,"url":"picture/fig_surface5-5.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"采用PBE交换关联泛函和自旋极化，再给体系加上0.1 V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","attributes":{},"skip":false,"key":"1.1.15.5"},{"backlink":"abacus-surface6.html#fig1.1.16.1","level":"1.1.16","list_caption":"Figure: 一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","alt":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","nro":14,"url":"picture/fig_surface6-1.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","attributes":{},"skip":false,"key":"1.1.16.1"},{"backlink":"abacus-surface6.html#fig1.1.16.2","level":"1.1.16","list_caption":"Figure: 静电势（Electrostatic Potential）沿超胞Z轴变化图","alt":"静电势（Electrostatic Potential）沿超胞Z轴变化图","nro":15,"url":"picture/fig_surface6-2.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"静电势（Electrostatic Potential）沿超胞Z轴变化图","attributes":{},"skip":false,"key":"1.1.16.2"},{"backlink":"develop-path4.html#fig1.2.9.1","level":"1.2.9","list_caption":"Figure: ","alt":" ","nro":16,"url":"picture/fig_path4-1.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":" ","attributes":{},"skip":false,"key":"1.2.9.1"},{"backlink":"develop-path4.html#fig1.2.9.2","level":"1.2.9","list_caption":"Figure: PW_Basis::distribute_r()：设一个pool中有5个processors","alt":"PW_Basis::distribute_r()：设一个pool中有5个processors","nro":17,"url":"picture/fig_path4-2.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"PW_Basis::distribute_r()：设一个pool中有5个processors","attributes":{},"skip":false,"key":"1.2.9.2"},{"backlink":"develop-path4.html#fig1.2.9.3","level":"1.2.9","list_caption":"Figure: this->count_pw_st(st_length2D, st_bottom2D)","alt":"this->count_pw_st(st_length2D, st_bottom2D)","nro":18,"url":"picture/fig_path4-3.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"this->count_pw_st(st_length2D, st_bottom2D)","attributes":{},"skip":false,"key":"1.2.9.3"},{"backlink":"develop-path5.html#fig1.2.10.1","level":"1.2.10","list_caption":"Figure: 善用Ctrl+F","alt":"善用Ctrl+F","nro":19,"url":"picture/fig_path5-9.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"善用Ctrl+F","attributes":{},"skip":false,"key":"1.2.10.1"},{"backlink":"develop-path5.html#fig1.2.10.2","level":"1.2.10","list_caption":"Figure: klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","alt":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","nro":20,"url":"picture/fig_path5-10.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","attributes":{},"skip":false,"key":"1.2.10.2"},{"backlink":"develop-path5.html#fig1.2.10.3","level":"1.2.10","list_caption":"Figure: klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","alt":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","nro":21,"url":"picture/fig_path5-11.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","attributes":{},"skip":false,"key":"1.2.10.3"},{"backlink":"develop-path5.html#fig1.2.10.4","level":"1.2.10","list_caption":"Figure: 1-dimensional example","alt":"1-dimensional example","nro":22,"url":"picture/fig_path5-12.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"1-dimensional example","attributes":{},"skip":false,"key":"1.2.10.4"},{"backlink":"develop-path5.html#fig1.2.10.5","level":"1.2.10","list_caption":"Figure: 2-dimensional example","alt":"2-dimensional example","nro":23,"url":"picture/fig_path5-13.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"2-dimensional example","attributes":{},"skip":false,"key":"1.2.10.5"}]},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"develop-path3.md","mtime":"2023-10-04T15:11:45.401Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-10-04T15:29:41.868Z"},"basePath":".","book":{"language":""}});
});
diff --git a/_book/develop-path4.html b/_book/develop-path4.html
index 1840948c..2b9cddf9 100644
--- a/_book/develop-path4.html
+++ b/_book/develop-path4.html
@@ -750,14 +750,14 @@ Driver
-Driver::atomic_world()
-Driver::driver_run()
-多层继承：Init() functions in esolver class
-Trigger: ESolver_FP::Init()
-平面波格点初始化：PW_Basis:: initgrids()
+Driver
+Driver::atomic_world()
+Driver::driver_run()
+多层继承：Init() functions in esolver class
+Trigger: ESolver_FP::Init()
+平面波格点初始化：PW_Basis:: initgrids()
完成了 INPUT 和 STRU，以及赝势文件的读取环节，接下来我们来到平面波的初始化设置相关部分。
-void ESolver_FP::Init(Input& inp, UnitCell& cell)
+ void ESolver_FP::Init(Input& inp, UnitCell& cell)
{
....
if (inp.nx * inp.ny * inp.nz == 0)
@@ -782,7 +782,7 @@ virtual void initgrids(const double lat0_in,const ModuleBase::Matrix3 latvec_in,
+ virtual void initgrids(const double lat0_in,const ModuleBase::Matrix3 latvec_in,
const double gridecut)
{
// generation of nx, ny and nz are omitted here
@@ -868,7 +868,7 @@ }
❗ 注意：这里还完成了倒空间格点数量 fftnx, fftny 和 fftnz 的赋值。因为 FFT 变换前后的格点数量一般相同，因此 fftnx = nx，fftny = ny，...。
-
+图 1. 然后对平面波在 MPI 进程间进行分发：
//module_esolver/esolver_fp.cpp
void ESolver_FP::Init(Input& inp, UnitCell& cell)
@@ -889,9 +889,9 @@ ::
timer::tick(this->classname, "setuptransform");
}
-PW_Basis::setuptransform()（link）
-# 并行机制简述
-## 并行池
+PW_Basis::setuptransform()（link）
+并行机制简述
+并行池
到这里，我们不得不开始对平面波的 MPI 并行机制有一个大致的认识。在 ABACUS 中，CPU（=processor）首先根据不同的布里渊区 k 点分组被划分成不同的并行池（parallelizaiton pool），每个 pool 都包含几个 k 点，在每个 pool 里面会有完整的对该 k 点求解 Kohn-Sham 方程的过程。因此，在每个 pool 中采用一定数量的 CPU 进程来完成计算。在 INPUT 文件中，KPAR 参数决定了并行池的数量（即 pool 的个数）。换句话说，ABACUS 的 k 点并行机制为，将 k 点（设其数量为 nkpt）分配在 KPAR 个 pool 中，若一共有 nproc 个 processor，则：
- 每个 pool 有
nproc/KPAR 个 processor
@@ -899,7 +899,7 @@ ## MPI 进程编号：rank
+MPI 进程编号：rank
rank 是一个在 MPI 并行里常被用到的变量。在拥有不止一个 processor 的时候，每个 processor 都具有唯一的编号，称为 rank。如果在每个 processor 都有 rank 的基础上还定义了 pool，以及在每个 pool 中的 processor 数量，则 processor 除了有跨 pool 的全局 rank，也可以有 pool 之内的局部 rank，这部分内容见 module_base/global_variable.cpp:
int NPROC = 1;
int KPAR = 1;
@@ -926,7 +926,7 @@ }
}
-## 并行策略
+并行策略
于是问题便到来：在并行条件下，代码究竟是如何执行的？
- 对于多核 CPU，是否运行在其上的所有程序都进行了并行化？
@@ -950,9 +950,9 @@ ## OpenMP-MPI 混合编程
+OpenMP-MPI 混合编程
通常来讲，尽管 OpenMP 提供了线程并行，但由于共享内存可能并不存在于 processors 之间，或 computer, nodes 之间，且没有适合的内存共享系统（multi-socket server），此时如果以 OpenMP 放心运行，则可能得出错误结果或直接报错——因为内存无法访问。对于这种情况，需要使用 MPI（Message passing interface）来维持无内存共享处理单元之间的信息交换，以及信息分发和分布计算，而在处理单元内部，即可以共享内存的域内，则可以通过 OpenMP 技术来进行线程级并行。
-# 实空间格点分发
+实空间格点分发
在简单介绍完并行机制后，我们知道，对于未显式以并行方式实现的函数，其运行将在每一个 processor。在接下来的平面波分发过程中，请始终牢记这一理念，尤其在 processor-local 变量和 processor-global 变量的传值过程中。
稍加回溯：
void ESolver_FP::Init(Input& inp, UnitCell& cell)
@@ -968,7 +968,7 @@ ## 实空间：PW_Basis::distribute_r()
+实空间：PW_Basis::distribute_r()
❗Attention
注意，此时实际调用的也是 PW_Basis_Big 而非 PW_Basis 的 distribute_r() 函数。
@@ -1011,8 +1011,8 @@ {
....
该判断不会 always true。因此 PW_Basis::distribute_r() 将 3D 实空间格点，按照 z 方向进行分发，分给了不同的 processors，并赋值 this->npz，this->nplane, this->startz_current 和 this->nrxx，意义分别为当前 processor 的 z 方向格点数量、xy 平面数量、z 格点的起始索引以及当前 processor 所分得实空间格点总数（分配后 z 方向格点 ×xy 平面格点）。
-
-## 倒空间：PW_Basis::distribute_g()
+图 2. PW_Basis::distribute_r()：设一个pool中有5个processors 倒空间：PW_Basis::distribute_g()
倒空间格点的分发采用了和实空间不同的方式，这主要是因为倒空间“球”的存在（ecutwfc 和 ecutrho），使得非空间中所有点都需要考虑在内，而实空间则并非如此。更一般而言，有限的实空间带来无限的倒空间（即实空间 delta 函数需要无限数量的平面波展开）延展，而有限的倒空间（倒空间 delta 点）带来无限的实空间延展（如一个平面波）。
🔧重构信息
@@ -1066,7 +1066,7 @@
delete
[] st_bottom2D; delete[] st_length2D;
}
-### 分发最小单元：“棍子” - 准备工作
+分发最小单元：“棍子” - 准备工作
穿过布里渊区的整数点（2pi/a 的整数倍）都代表一个三个 index 的平面波，而一系列的点在截断半径以内沿着某个方向就组成了所谓的“stick”（代表平面波集合的“棍子”，一个“棍子”包含了多个平面波，简称就叫“棍子”）。
PW_Basis::count_pw_st() 函数（Link）计算了每个(x,y)对应的“棍子”的底部和“长度”，即对倒空间只分辨(x,y)，则会得到沿 z 方向的点的集合，被称为“棍子”。而“棍子”区域内部每一个点都代表一个平面波。“棍子”的底部对应于最小的 iz 值，“根子”的长度则为当前(x,y)所包含的平面波数量：
for (int ix = ix_start; ix <= ix_end; ++ix)
@@ -1098,7 +1098,7 @@ }
}
-
+图 3. this->count_pw_st(st_length2D, st_bottom2D) 在倒空间分发平面波时，由于 x/y/z 均等在正负半轴 span，因此常常会涉及到 C++ 不支持负数索引的问题（btw: Python 和 FORTRAN 支持负数索引，但支持方式不同），ABACUS 当前所采取的策略是：
if (x<0) x += this->nx; if (y<0) y += this->ny; if (z<0) z += this->nz;
@@ -1107,7 +1107,7 @@ ### “棍子”的分发和分发记录
+“棍子”的分发和分发记录
PW_Basis::collect_st() 和 PW_Basis::divide_sticks_1() 分别排序与分发“棍子”到不同 processor：
- 按照棍子从长到短顺序进行排序，即
st_length2D 由大到小排序，然后适用于 st_bottom2D 等变量
@@ -1136,7 +1136,7 @@ this
->nstnz = this->nst * this->nz;
....
-### 映射表：OOP？
+映射表：OOP？
在倒空间平面波的分发过程中，共建立过四个映射表，分别是 this->fftixy2ip, this->istot2ixy, this->ig2isz 和 this->is2fftixy，其意义分别为：
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diff --git a/_book/develop-path1.html b/_book/develop-path1.html
index 1de92b86..d41c1be3 100644
--- a/_book/develop-path1.html
+++ b/_book/develop-path1.html
@@ -1112,8 +1112,8 @@ <
Input_Conv::Convert()
这个函数实现了从 Input 类对象的数据成员到 GlobalV 和 GlobalC 等全局变量集合的转换。相当于从 Input 到 GlobalV 和 GlobalC，以及其他直接的类的参数上载：
-其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
+其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
void Input_Conv::Convert(void)
{
....
@@ -1308,7 +1308,7 @@
不要忘记我们已经完成 Driver::reading() 函数内容，到达 Driver::atomic_world()。这一点从本文档设置的分级目录中也可以看得到。
-cppvoid Driver::init()
+void Driver::init()
{
this->reading();
this->atomic_world(); // <- here!
@@ -1518,7 +1518,7 @@ 从 SIAB 到 ABACUS（一）：准备工作（施工中 🚧）
下篇：Introduction to ABACUS: Path to PW calculation - Part 2
@@ -1562,7 +1562,7 @@ No results matching "
var gitbook = gitbook || [];
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index 191dfe74..d829579b 100644
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@@ -1028,7 +1028,7 @@ // a(i) is lattice vector
}
-我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
+我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
UnitCell::read_atom_positions()
🔧重构思考
@@ -1042,7 +1042,7 @@
::
GlobalFunc::READ_VALUE( ifpos, Coordinate);
STRU 第二行指定坐标类型，被读取为 UnitCell::Coordinate。UnitCell::Coordinate 在 STRU 里有不同选项，⚙ 决定原子的具体位置和单位：
-if(Coordinate != "Cartesian"
+ if(Coordinate != "Cartesian"
&& Coordinate != "Direct"
&& Coordinate != "Cartesian_angstrom"
&& Coordinate != "Cartesian_au"
@@ -1092,7 +1092,7 @@ int na = 0;
+ int na = 0;
this->nat = 0;
assert(ntype>0);
for (int it = 0;it < ntype; it++)
@@ -1105,7 +1105,7 @@ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
bool sequence_match = false;
for(int it2=0; it2<ntype; it2++)
{
@@ -1121,7 +1121,7 @@ }
读取当前原子类型的 starting_magnetization、原子总数 na
-ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
...
ModuleBase::GlobalFunc::READ_VALUE(ifpos, na);
this->atoms[it].na = na;
@@ -1149,17 +1149,17 @@ [
it].m_loc_ = new ModuleBase::Vector3<double>[na];
⚙ 然后在 ATOMIC_POSITIONS 中读取：
-atoms[it].mass = this->atom_mass[it];
+ atoms[it].mass = this->atom_mass[it];
❗ 此处的 atoms[it].mass 与 this->atom_mass[it] 的用法与 atomis[it].label 与 this->atom_label[it] 不同：传值 vs 核对。
接下来读取类中每个原子的速度信息，在做分子动力学模拟的时候可能需要用到：
-for (int ia = 0;ia < na; ia++)
+ for (int ia = 0;ia < na; ia++)
{
ifpos >> v.x >> v.y >> v.z;
然而，当前 STRU 文件在 ATOMIC_POSITIONS 的设计比较复杂，其可以包括任何一组 atom-specific 数据，且数量和顺序均不受限制，这导致判断条件变得复杂，详见 module_cell/read_atoms.cpp:line 536 - 567（link）。
atoms[it].mag 的赋值并非直接读取：
-else if ( tmpid == "mag" || tmpid == "magmom")
+ else if ( tmpid == "mag" || tmpid == "magmom")
{
set_element_mag_zero = true;
double tmpamg=0; ifpos >> tmpamg;
@@ -1185,7 +1185,7 @@ }
⚙ 若 mag/magmom 后有一个值，则读取其值赋给 atoms[it]::mag[ia]，将 input_vec_mag 置为 false，若有三个值，则三个值依次被传入 atoms[it].m_loc_[ia].x, atoms[it].m_loc_[ia].y 和 atoms[it].m_loc_[ia].z，并将 input_vec_mag 置为 true，之后其向量模长为 atoms[it]::mag[ia]，然后在使用 angle1, angle2 来重新生成 mag。
-if(GlobalV::NSPIN==4)
+ if(GlobalV::NSPIN==4)
{
if(GlobalV::NONCOLIN)
{
@@ -1227,7 +1227,7 @@ pw.x input description
ABACUS 对 nspin=4 情况的参数处理：
//module_io/input_conv.cpp line 376
if (INPUT.noncolin || INPUT.lspinorb)
@@ -1312,7 +1312,7 @@
UnitCell::setup_cell(): the rest, and an example of backtracking unclear variable
离开 STRU 文件的解析部分，接下来计算了初始磁化强度：
-//after read STRU, calculate initial total magnetization when NSPIN=2
+ //after read STRU, calculate initial total magnetization when NSPIN=2
if(GlobalV::NSPIN == 2 && !GlobalV::TWO_EFERMI)
{
for(int it = 0;it<this->ntype; it++)
@@ -1326,31 +1326,25 @@ if (std::abs(INPUT.nupdown) > 1e-6)
- {
- GlobalV::TWO_EFERMI = true;
- GlobalV::nupdown = INPUT.nupdown;
- }
-
-因此 GlobalV::TWO_EFERMI 变量实际依赖于 INPUT.nupdown。
-
-- 接下来在
module_io/input.cpp 中寻找含 INPUT.nupdown 的 if(strcmp(...)) 单元，查看在 INPUT 文件中是何参数赋予其具体值：
-
-else if (strcmp("nupdown", word) == 0)
+在 module_io/input_conv.cpp 中寻找该变量，是何变量赋其值，发现： if (std::abs(INPUT.nupdown) > 1e-6)
{
- read_value(ifs, nupdown);
- }
+ GlobalV::TWO_EFERMI = true;
+ GlobalV::nupdown = INPUT.nupdown;
+ }
-即 INPUT.nupdown 在 INPUT 中也为 nupdown。接下来打开 Full keyword list 寻找其解释。
-
+ 因此 GlobalV::TWO_EFERMI 变量实际依赖于 INPUT.nupdown。
+接下来在 module_io/input.cpp 中寻找含 INPUT.nupdown 的 if(strcmp(...)) 单元，查看在 INPUT 文件中是何参数赋予其具体值： else if (strcmp("nupdown", word) == 0)
+ {
+ read_value(ifs, nupdown);
+ }
+
+即 INPUT.nupdown 在 INPUT 中也为 nupdown。接下来打开 Full keyword list 寻找其解释。
得到结果，即 nupdown 为 spin up 和 spin down 电子数量差值：
因此该部分逻辑为：若未使用 nupdown 来指定单电子数量，则对每种原子内每个原子，累加其 mag/magmom，即磁矩模长，赋予 GlobalV::nupdown。❗ 但对于两种方式均赋予，但值不一致的情况未进行处理。
接下来根据在 STRU 中读取的晶胞参数，计算晶胞体积，并计算倒空间矢量（在上篇中已经对 latvec, G, GT, GGT 有所介绍，invGGT 的意义也不言自明）：
-this->omega = std::abs( latvec.Det() ) * this->lat0 * lat0 * lat0 ;
+ this->omega = std::abs( latvec.Det() ) * this->lat0 * lat0 * lat0 ;
this->GT = latvec.Inverse();
this->G = GT.Transpose();
@@ -1442,7 +1436,7 @@ =
static_cast<ModulePW::PW_Basis_Big*>(pw_rho);
对于 ESolver 本身，其指针对象 p_esolver 实际上也有类似操作：
-//Some API to operate E_Solver
+ //Some API to operate E_Solver
void init_esolver(ESolver*& p_esolver)
{
//determine type of esolver based on INPUT information
@@ -1907,7 +1901,7 @@ Introduction to ABACUS: Path to PW calculation - Part 1
下篇：Introduction to ABACUS: Path to PW calculation - Part 3
@@ -1951,7 +1945,7 @@ No results matching "
var gitbook = gitbook || [];
gitbook.push(function() {
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st_bottom2D)","attributes":{},"skip":false,"key":"1.2.9.3"},{"backlink":"develop-path5.html#fig1.2.10.1","level":"1.2.10","list_caption":"Figure: 善用Ctrl+F","alt":"善用Ctrl+F","nro":19,"url":"picture/fig_path5-9.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"善用Ctrl+F","attributes":{},"skip":false,"key":"1.2.10.1"},{"backlink":"develop-path5.html#fig1.2.10.2","level":"1.2.10","list_caption":"Figure: klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","alt":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","nro":20,"url":"picture/fig_path5-10.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","attributes":{},"skip":false,"key":"1.2.10.2"},{"backlink":"develop-path5.html#fig1.2.10.3","level":"1.2.10","list_caption":"Figure: klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","alt":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","nro":21,"url":"picture/fig_path5-11.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","attributes":{},"skip":false,"key":"1.2.10.3"},{"backlink":"develop-path5.html#fig1.2.10.4","level":"1.2.10","list_caption":"Figure: 1-dimensional example","alt":"1-dimensional example","nro":22,"url":"picture/fig_path5-12.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"1-dimensional example","attributes":{},"skip":false,"key":"1.2.10.4"},{"backlink":"develop-path5.html#fig1.2.10.5","level":"1.2.10","list_caption":"Figure: 2-dimensional example","alt":"2-dimensional example","nro":23,"url":"picture/fig_path5-13.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"2-dimensional example","attributes":{},"skip":false,"key":"1.2.10.5"}]},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"develop-path2.md","mtime":"2023-10-04T14:37:12.149Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-10-04T15:29:41.868Z"},"basePath":".","book":{"language":""}});
});
diff --git a/_book/develop-path3.html b/_book/develop-path3.html
index b8de33d9..09176394 100644
--- a/_book/develop-path3.html
+++ b/_book/develop-path3.html
@@ -750,11 +750,11 @@ Driver
-Driver::atomic_world()
-Driver::driver_run()
-多层继承：Init() functions in esolver class
-Trigger: ESolver_FP::Init()
+Driver
+Driver::atomic_world()
+Driver::driver_run()
+多层继承：Init() functions in esolver class
+Trigger: ESolver_FP::Init()
承接上篇中已经导入的结构信息，以及了解到构造函数及其伴随的变量初始化和 ABACUS 里应用到的 C++ 多态编程，接下来即将（逐渐）步入 ABACUS 的核心内容。我们暂时跳过位于 source/driver_run.cpp:driver_run() 的：
// 3. For these two types of calculations
// nothing else need to be initialized
@@ -830,14 +830,14 @@ }
同理，ESolver_KS 的数据成员，也被 ESolver_KS_PW 继承。ESolver_FP::Init() 首先调用 UnitCell::read_pseudo() 函数进行赝势文件读取，而将赝势文件读取任务放在 FP 层级下，也暗示对于 ABACUS 的第一性原理方法实现来讲，都需要使用赝势。
-Pseudopotential import: UnitCell::read_pseudo()
+Pseudopotential import: UnitCell::read_pseudo()
void UnitCell::read_pseudo(std::ofstream &ofs)
{
read_cell_pseudopots(GlobalV::global_pseudo_dir, ofs);
在解读赝势文件读取功能之前，首先需要对赝势文件的结构和信息做一定程度的了解。
-# ONCV pseudopotential file
-## Section 0: Norm-conserving conditions, generation of pseudopotential and header of exact UPF file
+ONCV pseudopotential file
+Section 0: Norm-conserving conditions, generation of pseudopotential and header of exact UPF file
赝势的意义不言自明，其中模守恒赝势需满足如下条件：
- （赝势得到的能级和全电子方法求解的能级一样，这里 ps 代表 pseudopotentials）
@@ -852,7 +852,7 @@ V_l(r)=\frac{1}{\phi^\text{ps}_l(r)}[\epsilon^\text{ps}_l-\frac{\hbar^2}{2m}\frac{l(l+1)}{r^2}+\frac{\hbar^2}{2m}\frac{d^2}{dr^2}]\phi^\text{ps}_l(r)，解得。
- 扣除中 Hartree、xc 部分，得到：。
-更多细节见
+更多细节见：www.tcm.phy.cam.ac.uk
<UPF version="2.0.1">
<PP_INFO>
<!-- omitted information here -->
@@ -865,8 +865,8 @@ <!-- -->
从 UPF 文件（注意 UPF 文件也有不同的版本，目前 ABACUS 都支持，若有不支持的，可以提 Github 的 issues 进行讨论）开始，截止到 <PP_HEADER> 之前，提供了赝势文件的作者信息，引用信息以及生成赝势文件所使用的程序和相应输入文件，并附带输入文件参数中的解释。由于此块内容对实际计算并不起作用，因此暂时略过。
-## Section 1:
-<PP_HEADER
+Section 1:
+ <PP_HEADER
generated="Generated using ONCVPSP code by D. R. Hamann" author="Martin Schlipf and Francois Gygi"
date="150105" comment=""
element="Al"
@@ -890,8 +890,8 @@ number_of_proj
="4"/>
<PP_HEADER> 部分尽管已经位于所谓“not human readable”区域，但也并非如此。这部分“标签”（HTML 语境）/block 实际上包含了众多精简过的信息，如元素名称（element）、赝势类型（pseudo_type，模守恒，norm-conserving，NC），相对论效应（relativistic），是否为超软赝势等等信息。当前 Al 理论上其原子序数 13，因此有 13 个电子，但此处 z_valence 参数为 11，即有两个 1s 电子被赝化，只留下 2s, 2p, 3s, 3p 电子共 2+6+2+1 个。对于某些元素，甚至有大核赝势与小核赝势之分，根据赝化电子数量不同进行区分。显而易见地，赝化电子数量越多，则计算量越小，但计算结果的精确程度可能更低。
-## Section 2:
-<PP_MESH>
+Section 2:
+ <PP_MESH>
<PP_R type="real" size=" 602" columns="8">
0.0000 0.0100 0.0200 0.0300 0.0400 0.0500 0.0600 0.0700
<!-- omitted information here -->
@@ -907,8 +907,8 @@ </PP_MESH>
这部分开始出现了关于实空间格点相关量的定义。在 tag 中不仅指定数据类型为实数，也指定当前数据的长度（size），以及数据存储的列数（columns = 8）。PP_R 为格点坐标，PP_RAB 则为格点间距。
-## Section 3:
-<PP_LOCAL type="real" size=" 602" columns="4">
+Section 3:
+ <PP_LOCAL type="real" size=" 602" columns="4">
-4.5793174225E+01 -4.5788454271E+01 -4.5774276797E+01 -4.5750659428E+01
<!-- omitted information here -->
-3.6912752197E+00 -3.6850921941E+00 -3.6789298138E+00 -3.6727880140E+00
@@ -917,8 +917,8 @@ <PP_LOCAL>
部分开始，正式开始写入赝势的具体数值，建立在 <PP_R> 和 <PP_RAB> 所描述的实空间格点上。。<PP_LOCAL> 正是赝势的局域势部分。
-## Section 4:
-<PP_NONLOCAL>
+Section 4:
+ <PP_NONLOCAL>
<PP_BETA.1
type="real"
size=" 602"
@@ -938,8 +938,8 @@ cutoff_radius_index
=" 246" cutoff_radius=" 2.4500000000E+00" >
<!-- omitted information here -->
</PP_BETA.2>
- <PP_BETA.3 type="real" size=" 602" columns="4" index="3" angular_momentum="1"<strong>
-</strong> cutoff_radius_index=" 246" cutoff_radius=" 2.4500000000E+00" >
+ <PP_BETA.3 type="real" size=" 602" columns="4" index="3" angular_momentum="1"
+ cutoff_radius_index=" 246" cutoff_radius=" 2.4500000000E+00" >
<!-- omitted information here -->
</PP_BETA.3>
<PP_BETA.4 type="real" size=" 602" columns="4" index="4" angular_momentum="1"
@@ -956,7 +956,7 @@ \hat{V}^\text{NL}=\sum_{ij}{|\beta_i\rangle D_{ij}\langle\beta_j|}。其中一般被称为非局域势投影子（projector）。
-## Section 5: and
+Section 5: and
<PP_PSWFC>
</PP_PSWFC>
<PP_RHOATOM type="real" size=" 602" columns="4">
@@ -975,7 +975,7 @@ |\beta\rangle和 pswfc 已经乘径向坐标。
-# UnitCell::read_cell_pseudopots()
+UnitCell::read_cell_pseudopots()
link to Github -> link
void UnitCell::read_cell_pseudopots(const std::string &pp_dir, std::ofstream &log)
{
@@ -1030,7 +1030,7 @@ while (ifs.good())
+ while (ifs.good())
{
ifs >> dummy;
if(dummy=="<PP_HEADER>")
@@ -1044,7 +1044,7 @@ if ( ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_MESH>") )
+ if ( ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_MESH>") )
{
read_pseudo_mesh(ifs);
ModuleBase::GlobalFunc::SCAN_END(ifs, "</PP_MESH>");
@@ -1052,7 +1052,7 @@ if (this->nlcc)
+ if (this->nlcc)
{
ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_NLCC>");
read_pseudo_nlcc(ifs);
@@ -1061,12 +1061,12 @@ ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_LOCAL>");
+ ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_LOCAL>");
read_pseudo_local(ifs);
ModuleBase::GlobalFunc::SCAN_END(ifs, "</PP_LOCAL>");
与 类似的还有 , , , 从 则可以读取旋轨耦合相关信息：
-if (has_so)
+ if (has_so)
{
ModuleBase::GlobalFunc::SCAN_BEGIN (ifs,"<PP_ADDINFO>");
read_pseudo_so (ifs);
@@ -1140,7 +1140,7 @@ if(error==0)
+ if(error==0)
{
if(this->atoms[i].flag_empty_element) upf.set_empty_element();
error_ap = upf.average_p(GlobalV::soc_lambda);
@@ -1148,7 +1148,7 @@ if(GlobalV::MY_RANK==0)
+ if(GlobalV::MY_RANK==0)
{
atoms[i].ncpp.set_pseudo_nc( upf );
....
@@ -1178,7 +1178,7 @@ }
该函数属于类 pseudo_nc，而 pseudo_nc 对象为 atom 的数据成员，atoms 则为 UnitCell 的数据成员。pseudo_nc::set_pseudo_h()，pseudo_nc::set_pseudo_atom 和 pseudo_nc::set_pseudo_vl 的内容在此省略，但其分别为将 Hamilton, 原子性质和 Vlocal 相关数据从 upf 对象拷贝。之后(1)使用 lll 刷新为 upf 对象的 projectors 的角动量，然后计算出磁角动量区分时的 projector 个数。(2)取所有 projector 衰减到 0 时候的最大最普适半径。
-# 赝势信息后处理
+赝势信息后处理
回到 module_cell/unitcell.cpp line 663，接下来为每个原子创建目录，在目录中写 [原子label].NONLOCAL 文件。[label].NONLOCAL 文件中内容包含 <HEADER>, <DIJ> 和 <PP_BETA> 三个 tag。
<HEADER> 中包含内容：
ofs << "<HEADER>" << std::endl;
@@ -1222,21 +1222,61 @@ }
ofs << "</PP_BETA>" << std::endl;
-# 赝势信息分发：UnitCell::bcast_unitcell2(void)
+赝势信息分发：UnitCell::bcast_unitcell2(void)
#ifdef __MPI
+接下来对赝势信息进行MPI进程（processor）间的分发：
+#ifdef __MPI
+ bcast_unitcell2();
+#endif
+
+// module_cell/unitcell.cpp:bcast_unitcell2()
+void UnitCell::bcast_unitcell2(void)
+{
+ for (int i = 0; i < ntype; i++)
+ {
+ atoms[i].bcast_atom2();
+ }
+ return;
+}
+
+// module_cell/atom_spec.cpp:Atom::bcast_atom2()
+void Atom::bcast_atom2()
+{
+ this->ncpp.bcast_atom_pseudo();
+}
+
+// module_cell/atom_pseudo.cpp::Atom_pseudo::bcast_atom_pseudo()
+void Atom_pseudo::bcast_atom_pseudo(void)
+{
+....
+ Parallel_Common::bcast_int( lmax );
+....
+ Parallel_Common::bcast_double( etotps );
+....
+ Parallel_Common::bcast_bool( tvanp );
+....
+ Parallel_Common::bcast_string( psd );
+....
+ // below two 'bcast_double' lines of codes seem to have bugs,
+ // on some computers, the code will stuck here for ever.
+ // mohan note 2021-04-28
+ Parallel_Common::bcast_double( dion.c , nbeta * nbeta);
+ Parallel_Common::bcast_double( betar.c, nr * nc );
+}
+
#endif
-# 赝势信息核对
+赝势信息核对
接下来跨原子种类检验泛函是否一致：
-for(int it=0; it<ntype; it++)
+ for(int it=0; it<ntype; it++)
{
if(atoms[0].ncpp.xc_func !=atoms[it].ncpp.xc_func)
{
-# STRU 结构检查：UnitCell::check_structure()
+STRU 结构检查：UnitCell::check_structure()
检验结构中任意两原子之间距离是否大于其固定倍数（<1）的共价半径和，
-check_structure(GlobalV::MIN_DIST_COEF);
+ check_structure(GlobalV::MIN_DIST_COEF);
-# 计算轨道数：UnitCell::cal_natomwfc()
+计算轨道数：UnitCell::cal_natomwfc()
UnitCell::cal_natomwfc() 函数计算所有种类的原子轨道数量加和，对于非 nspin=4，即非 soc（自旋轨道耦合）情况，角量子数 l 和 s 非耦合，l 单独可以作为好的量子数来区分量子态，因此对于每个赝势中定义的 wfc，若其对应 occupation 大于等于 0（即有效 wfc），则对应于其角量子数 l，轨道数量增加 2l+1，即计数其磁量子数 m，也相当于对 alpha 和 beta spin 的单独计数。对于 nspin=4 的情况，若考虑 soc，则轨道数对 j=l+s 的情况，当前原子种类当前角量子数对应轨道数量记为 2l+1+1，否则为 2l+1。对于非 soc 但 nspin=4，当前原子种类轨道当前角量子数对应轨道数量记(2l+1)*2：
void UnitCell::cal_natomwfc(std::ofstream &log)
{
@@ -1291,9 +1331,9 @@ 计算跨原子种类最大角量子数 UnitCell::lmax 和某 l 对应最大 zeta 数 UnitCell::nmax，以及跨原子种类的类内 zeta 数总和最大值 UnitCell::nmax_total
寻找赝势中最大角量子数 UnitCell::lmax_ppwf。
-# 价电子数核对
+价电子数核对
核对赝势中定义的价电子数与 ABACUS 预置库中原子的最小价电子数
-# 获取最大格点数量：UnitCell::cal_meshx()
+获取最大格点数量：UnitCell::cal_meshx()
计算跨原子种类的最大格点数量，存储在 UnitCell::meshx 中，目前 ABACUS 代码中变量命名后缀 x 可能代表 max，正如之前看到 npwx 等。
至此，我们离开函数 UnitCell::read_pseudo()，回到 ModuleESolver::ESolver_FP::Init() 函数。
@@ -1304,7 +1344,7 @@ Introduction to ABACUS: Path to PW calculation - Part 2
下篇：Introduction to ABACUS: Path to PW calculation - Part 4
@@ -1348,7 +1388,7 @@ No results matching "
var gitbook = gitbook || [];
gitbook.push(function() {
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example","attributes":{},"skip":false,"key":"1.2.10.5"}]},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"develop-path3.md","mtime":"2023-10-04T15:11:45.401Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-10-04T15:29:41.868Z"},"basePath":".","book":{"language":""}});
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diff --git a/_book/develop-path4.html b/_book/develop-path4.html
index 1840948c..2b9cddf9 100644
--- a/_book/develop-path4.html
+++ b/_book/develop-path4.html
@@ -750,14 +750,14 @@ Driver
-Driver::atomic_world()
-Driver::driver_run()
-多层继承：Init() functions in esolver class
-Trigger: ESolver_FP::Init()
-平面波格点初始化：PW_Basis:: initgrids()
+Driver
+Driver::atomic_world()
+Driver::driver_run()
+多层继承：Init() functions in esolver class
+Trigger: ESolver_FP::Init()
+平面波格点初始化：PW_Basis:: initgrids()
完成了 INPUT 和 STRU，以及赝势文件的读取环节，接下来我们来到平面波的初始化设置相关部分。
-void ESolver_FP::Init(Input& inp, UnitCell& cell)
+ void ESolver_FP::Init(Input& inp, UnitCell& cell)
{
....
if (inp.nx * inp.ny * inp.nz == 0)
@@ -782,7 +782,7 @@ virtual void initgrids(const double lat0_in,const ModuleBase::Matrix3 latvec_in,
+ virtual void initgrids(const double lat0_in,const ModuleBase::Matrix3 latvec_in,
const double gridecut)
{
// generation of nx, ny and nz are omitted here
@@ -868,7 +868,7 @@ }
❗ 注意：这里还完成了倒空间格点数量 fftnx, fftny 和 fftnz 的赋值。因为 FFT 变换前后的格点数量一般相同，因此 fftnx = nx，fftny = ny，...。
-
+图 1. 然后对平面波在 MPI 进程间进行分发：
//module_esolver/esolver_fp.cpp
void ESolver_FP::Init(Input& inp, UnitCell& cell)
@@ -889,9 +889,9 @@ ::
timer::tick(this->classname, "setuptransform");
}
-PW_Basis::setuptransform()（link）
-# 并行机制简述
-## 并行池
+PW_Basis::setuptransform()（link）
+并行机制简述
+并行池
到这里，我们不得不开始对平面波的 MPI 并行机制有一个大致的认识。在 ABACUS 中，CPU（=processor）首先根据不同的布里渊区 k 点分组被划分成不同的并行池（parallelizaiton pool），每个 pool 都包含几个 k 点，在每个 pool 里面会有完整的对该 k 点求解 Kohn-Sham 方程的过程。因此，在每个 pool 中采用一定数量的 CPU 进程来完成计算。在 INPUT 文件中，KPAR 参数决定了并行池的数量（即 pool 的个数）。换句话说，ABACUS 的 k 点并行机制为，将 k 点（设其数量为 nkpt）分配在 KPAR 个 pool 中，若一共有 nproc 个 processor，则：
- 每个 pool 有
nproc/KPAR 个 processor
@@ -899,7 +899,7 @@ ## MPI 进程编号：rank
+MPI 进程编号：rank
rank 是一个在 MPI 并行里常被用到的变量。在拥有不止一个 processor 的时候，每个 processor 都具有唯一的编号，称为 rank。如果在每个 processor 都有 rank 的基础上还定义了 pool，以及在每个 pool 中的 processor 数量，则 processor 除了有跨 pool 的全局 rank，也可以有 pool 之内的局部 rank，这部分内容见 module_base/global_variable.cpp:
int NPROC = 1;
int KPAR = 1;
@@ -926,7 +926,7 @@ }
}
-## 并行策略
+并行策略
于是问题便到来：在并行条件下，代码究竟是如何执行的？
- 对于多核 CPU，是否运行在其上的所有程序都进行了并行化？
@@ -950,9 +950,9 @@ ## OpenMP-MPI 混合编程
+OpenMP-MPI 混合编程
通常来讲，尽管 OpenMP 提供了线程并行，但由于共享内存可能并不存在于 processors 之间，或 computer, nodes 之间，且没有适合的内存共享系统（multi-socket server），此时如果以 OpenMP 放心运行，则可能得出错误结果或直接报错——因为内存无法访问。对于这种情况，需要使用 MPI（Message passing interface）来维持无内存共享处理单元之间的信息交换，以及信息分发和分布计算，而在处理单元内部，即可以共享内存的域内，则可以通过 OpenMP 技术来进行线程级并行。
-# 实空间格点分发
+实空间格点分发
在简单介绍完并行机制后，我们知道，对于未显式以并行方式实现的函数，其运行将在每一个 processor。在接下来的平面波分发过程中，请始终牢记这一理念，尤其在 processor-local 变量和 processor-global 变量的传值过程中。
稍加回溯：
void ESolver_FP::Init(Input& inp, UnitCell& cell)
@@ -968,7 +968,7 @@ ## 实空间：PW_Basis::distribute_r()
+实空间：PW_Basis::distribute_r()
❗Attention
注意，此时实际调用的也是 PW_Basis_Big 而非 PW_Basis 的 distribute_r() 函数。
@@ -1011,8 +1011,8 @@ {
....
该判断不会 always true。因此 PW_Basis::distribute_r() 将 3D 实空间格点，按照 z 方向进行分发，分给了不同的 processors，并赋值 this->npz，this->nplane, this->startz_current 和 this->nrxx，意义分别为当前 processor 的 z 方向格点数量、xy 平面数量、z 格点的起始索引以及当前 processor 所分得实空间格点总数（分配后 z 方向格点 ×xy 平面格点）。
-
-## 倒空间：PW_Basis::distribute_g()
+图 2. PW_Basis::distribute_r()：设一个pool中有5个processors 倒空间：PW_Basis::distribute_g()
倒空间格点的分发采用了和实空间不同的方式，这主要是因为倒空间“球”的存在（ecutwfc 和 ecutrho），使得非空间中所有点都需要考虑在内，而实空间则并非如此。更一般而言，有限的实空间带来无限的倒空间（即实空间 delta 函数需要无限数量的平面波展开）延展，而有限的倒空间（倒空间 delta 点）带来无限的实空间延展（如一个平面波）。
🔧重构信息
@@ -1066,7 +1066,7 @@
delete
[] st_bottom2D; delete[] st_length2D;
}
-### 分发最小单元：“棍子” - 准备工作
+分发最小单元：“棍子” - 准备工作
穿过布里渊区的整数点（2pi/a 的整数倍）都代表一个三个 index 的平面波，而一系列的点在截断半径以内沿着某个方向就组成了所谓的“stick”（代表平面波集合的“棍子”，一个“棍子”包含了多个平面波，简称就叫“棍子”）。
PW_Basis::count_pw_st() 函数（Link）计算了每个(x,y)对应的“棍子”的底部和“长度”，即对倒空间只分辨(x,y)，则会得到沿 z 方向的点的集合，被称为“棍子”。而“棍子”区域内部每一个点都代表一个平面波。“棍子”的底部对应于最小的 iz 值，“根子”的长度则为当前(x,y)所包含的平面波数量：
for (int ix = ix_start; ix <= ix_end; ++ix)
@@ -1098,7 +1098,7 @@ }
}
-
+图 3. this->count_pw_st(st_length2D, st_bottom2D) 在倒空间分发平面波时，由于 x/y/z 均等在正负半轴 span，因此常常会涉及到 C++ 不支持负数索引的问题（btw: Python 和 FORTRAN 支持负数索引，但支持方式不同），ABACUS 当前所采取的策略是：
if (x<0) x += this->nx; if (y<0) y += this->ny; if (z<0) z += this->nz;
@@ -1107,7 +1107,7 @@ ### “棍子”的分发和分发记录
+“棍子”的分发和分发记录
PW_Basis::collect_st() 和 PW_Basis::divide_sticks_1() 分别排序与分发“棍子”到不同 processor：
- 按照棍子从长到短顺序进行排序，即
st_length2D 由大到小排序，然后适用于 st_bottom2D 等变量
@@ -1136,7 +1136,7 @@ this
->nstnz = this->nst * this->nz;
....
-### 映射表：OOP？
+映射表：OOP？
在倒空间平面波的分发过程中，共建立过四个映射表，分别是 this->fftixy2ip, this->istot2ixy, this->ig2isz 和 this->is2fftixy，其意义分别为：
No results matching "
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diff --git a/_book/develop-path1.html b/_book/develop-path1.html
index 1de92b86..d41c1be3 100644
--- a/_book/develop-path1.html
+++ b/_book/develop-path1.html
@@ -1112,8 +1112,8 @@ <
Input_Conv::Convert()
这个函数实现了从 Input 类对象的数据成员到 GlobalV 和 GlobalC 等全局变量集合的转换。相当于从 Input 到 GlobalV 和 GlobalC，以及其他直接的类的参数上载：
-其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
+其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
void Input_Conv::Convert(void)
{
....
@@ -1308,7 +1308,7 @@
不要忘记我们已经完成 Driver::reading() 函数内容，到达 Driver::atomic_world()。这一点从本文档设置的分级目录中也可以看得到。
-cppvoid Driver::init()
+void Driver::init()
{
this->reading();
this->atomic_world(); // <- here!
@@ -1518,7 +1518,7 @@ 从 SIAB 到 ABACUS（一）：准备工作（施工中 🚧）
下篇：Introduction to ABACUS: Path to PW calculation - Part 2
@@ -1562,7 +1562,7 @@ No results matching "
var gitbook = gitbook || [];
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index 191dfe74..d829579b 100644
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@@ -1028,7 +1028,7 @@ // a(i) is lattice vector
}
-我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
+我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
UnitCell::read_atom_positions()
🔧重构思考
@@ -1042,7 +1042,7 @@
::
GlobalFunc::READ_VALUE( ifpos, Coordinate);
STRU 第二行指定坐标类型，被读取为 UnitCell::Coordinate。UnitCell::Coordinate 在 STRU 里有不同选项，⚙ 决定原子的具体位置和单位：
-if(Coordinate != "Cartesian"
+ if(Coordinate != "Cartesian"
&& Coordinate != "Direct"
&& Coordinate != "Cartesian_angstrom"
&& Coordinate != "Cartesian_au"
@@ -1092,7 +1092,7 @@ int na = 0;
+ int na = 0;
this->nat = 0;
assert(ntype>0);
for (int it = 0;it < ntype; it++)
@@ -1105,7 +1105,7 @@ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
bool sequence_match = false;
for(int it2=0; it2<ntype; it2++)
{
@@ -1121,7 +1121,7 @@ }
读取当前原子类型的 starting_magnetization、原子总数 na
-ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
...
ModuleBase::GlobalFunc::READ_VALUE(ifpos, na);
this->atoms[it].na = na;
@@ -1149,17 +1149,17 @@ [
it].m_loc_ = new ModuleBase::Vector3<double>[na];
⚙ 然后在 ATOMIC_POSITIONS 中读取：
-atoms[it].mass = this->atom_mass[it];
+ atoms[it].mass = this->atom_mass[it];
❗ 此处的 atoms[it].mass 与 this->atom_mass[it] 的用法与 atomis[it].label 与 this->atom_label[it] 不同：传值 vs 核对。
接下来读取类中每个原子的速度信息，在做分子动力学模拟的时候可能需要用到：
-for (int ia = 0;ia < na; ia++)
+ for (int ia = 0;ia < na; ia++)
{
ifpos >> v.x >> v.y >> v.z;
然而，当前 STRU 文件在 ATOMIC_POSITIONS 的设计比较复杂，其可以包括任何一组 atom-specific 数据，且数量和顺序均不受限制，这导致判断条件变得复杂，详见 module_cell/read_atoms.cpp:line 536 - 567（link）。
atoms[it].mag 的赋值并非直接读取：
-else if ( tmpid == "mag" || tmpid == "magmom")
+ else if ( tmpid == "mag" || tmpid == "magmom")
{
set_element_mag_zero = true;
double tmpamg=0; ifpos >> tmpamg;
@@ -1185,7 +1185,7 @@ }
⚙ 若 mag/magmom 后有一个值，则读取其值赋给 atoms[it]::mag[ia]，将 input_vec_mag 置为 false，若有三个值，则三个值依次被传入 atoms[it].m_loc_[ia].x, atoms[it].m_loc_[ia].y 和 atoms[it].m_loc_[ia].z，并将 input_vec_mag 置为 true，之后其向量模长为 atoms[it]::mag[ia]，然后在使用 angle1, angle2 来重新生成 mag。
-if(GlobalV::NSPIN==4)
+ if(GlobalV::NSPIN==4)
{
if(GlobalV::NONCOLIN)
{
@@ -1227,7 +1227,7 @@ pw.x input description
ABACUS 对 nspin=4 情况的参数处理：
//module_io/input_conv.cpp line 376
if (INPUT.noncolin || INPUT.lspinorb)
@@ -1312,7 +1312,7 @@
UnitCell::setup_cell(): the rest, and an example of backtracking unclear variable
离开 STRU 文件的解析部分，接下来计算了初始磁化强度：
-//after read STRU, calculate initial total magnetization when NSPIN=2
+ //after read STRU, calculate initial total magnetization when NSPIN=2
if(GlobalV::NSPIN == 2 && !GlobalV::TWO_EFERMI)
{
for(int it = 0;it<this->ntype; it++)
@@ -1326,31 +1326,25 @@ if (std::abs(INPUT.nupdown) > 1e-6)
- {
- GlobalV::TWO_EFERMI = true;
- GlobalV::nupdown = INPUT.nupdown;
- }
-
-因此 GlobalV::TWO_EFERMI 变量实际依赖于 INPUT.nupdown。
-
-- 接下来在
module_io/input.cpp 中寻找含 INPUT.nupdown 的 if(strcmp(...)) 单元，查看在 INPUT 文件中是何参数赋予其具体值：
-
-else if (strcmp("nupdown", word) == 0)
+在 module_io/input_conv.cpp 中寻找该变量，是何变量赋其值，发现： if (std::abs(INPUT.nupdown) > 1e-6)
{
- read_value(ifs, nupdown);
- }
+ GlobalV::TWO_EFERMI = true;
+ GlobalV::nupdown = INPUT.nupdown;
+ }
-即 INPUT.nupdown 在 INPUT 中也为 nupdown。接下来打开 Full keyword list 寻找其解释。
-
+ 因此 GlobalV::TWO_EFERMI 变量实际依赖于 INPUT.nupdown。
+接下来在 module_io/input.cpp 中寻找含 INPUT.nupdown 的 if(strcmp(...)) 单元，查看在 INPUT 文件中是何参数赋予其具体值： else if (strcmp("nupdown", word) == 0)
+ {
+ read_value(ifs, nupdown);
+ }
+
+即 INPUT.nupdown 在 INPUT 中也为 nupdown。接下来打开 Full keyword list 寻找其解释。
得到结果，即 nupdown 为 spin up 和 spin down 电子数量差值：
因此该部分逻辑为：若未使用 nupdown 来指定单电子数量，则对每种原子内每个原子，累加其 mag/magmom，即磁矩模长，赋予 GlobalV::nupdown。❗ 但对于两种方式均赋予，但值不一致的情况未进行处理。
接下来根据在 STRU 中读取的晶胞参数，计算晶胞体积，并计算倒空间矢量（在上篇中已经对 latvec, G, GT, GGT 有所介绍，invGGT 的意义也不言自明）：
-this->omega = std::abs( latvec.Det() ) * this->lat0 * lat0 * lat0 ;
+ this->omega = std::abs( latvec.Det() ) * this->lat0 * lat0 * lat0 ;
this->GT = latvec.Inverse();
this->G = GT.Transpose();
@@ -1442,7 +1436,7 @@ =
static_cast<ModulePW::PW_Basis_Big*>(pw_rho);
对于 ESolver 本身，其指针对象 p_esolver 实际上也有类似操作：
-//Some API to operate E_Solver
+ //Some API to operate E_Solver
void init_esolver(ESolver*& p_esolver)
{
//determine type of esolver based on INPUT information
@@ -1907,7 +1901,7 @@ Introduction to ABACUS: Path to PW calculation - Part 1
下篇：Introduction to ABACUS: Path to PW calculation - Part 3
@@ -1951,7 +1945,7 @@ No results matching "
var gitbook = gitbook || [];
gitbook.push(function() {
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st_bottom2D)","attributes":{},"skip":false,"key":"1.2.9.3"},{"backlink":"develop-path5.html#fig1.2.10.1","level":"1.2.10","list_caption":"Figure: 善用Ctrl+F","alt":"善用Ctrl+F","nro":19,"url":"picture/fig_path5-9.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"善用Ctrl+F","attributes":{},"skip":false,"key":"1.2.10.1"},{"backlink":"develop-path5.html#fig1.2.10.2","level":"1.2.10","list_caption":"Figure: klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","alt":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","nro":20,"url":"picture/fig_path5-10.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","attributes":{},"skip":false,"key":"1.2.10.2"},{"backlink":"develop-path5.html#fig1.2.10.3","level":"1.2.10","list_caption":"Figure: klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","alt":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","nro":21,"url":"picture/fig_path5-11.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","attributes":{},"skip":false,"key":"1.2.10.3"},{"backlink":"develop-path5.html#fig1.2.10.4","level":"1.2.10","list_caption":"Figure: 1-dimensional example","alt":"1-dimensional example","nro":22,"url":"picture/fig_path5-12.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"1-dimensional example","attributes":{},"skip":false,"key":"1.2.10.4"},{"backlink":"develop-path5.html#fig1.2.10.5","level":"1.2.10","list_caption":"Figure: 2-dimensional example","alt":"2-dimensional example","nro":23,"url":"picture/fig_path5-13.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"2-dimensional example","attributes":{},"skip":false,"key":"1.2.10.5"}]},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"develop-path2.md","mtime":"2023-10-04T14:37:12.149Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-10-04T15:29:41.868Z"},"basePath":".","book":{"language":""}});
});
diff --git a/_book/develop-path3.html b/_book/develop-path3.html
index b8de33d9..09176394 100644
--- a/_book/develop-path3.html
+++ b/_book/develop-path3.html
@@ -750,11 +750,11 @@ Driver
-Driver::atomic_world()
-Driver::driver_run()
-多层继承：Init() functions in esolver class
-Trigger: ESolver_FP::Init()
+Driver
+Driver::atomic_world()
+Driver::driver_run()
+多层继承：Init() functions in esolver class
+Trigger: ESolver_FP::Init()
承接上篇中已经导入的结构信息，以及了解到构造函数及其伴随的变量初始化和 ABACUS 里应用到的 C++ 多态编程，接下来即将（逐渐）步入 ABACUS 的核心内容。我们暂时跳过位于 source/driver_run.cpp:driver_run() 的：
// 3. For these two types of calculations
// nothing else need to be initialized
@@ -830,14 +830,14 @@ }
同理，ESolver_KS 的数据成员，也被 ESolver_KS_PW 继承。ESolver_FP::Init() 首先调用 UnitCell::read_pseudo() 函数进行赝势文件读取，而将赝势文件读取任务放在 FP 层级下，也暗示对于 ABACUS 的第一性原理方法实现来讲，都需要使用赝势。
-Pseudopotential import: UnitCell::read_pseudo()
+Pseudopotential import: UnitCell::read_pseudo()
void UnitCell::read_pseudo(std::ofstream &ofs)
{
read_cell_pseudopots(GlobalV::global_pseudo_dir, ofs);
在解读赝势文件读取功能之前，首先需要对赝势文件的结构和信息做一定程度的了解。
-# ONCV pseudopotential file
-## Section 0: Norm-conserving conditions, generation of pseudopotential and header of exact UPF file
+ONCV pseudopotential file
+Section 0: Norm-conserving conditions, generation of pseudopotential and header of exact UPF file
赝势的意义不言自明，其中模守恒赝势需满足如下条件：
- （赝势得到的能级和全电子方法求解的能级一样，这里 ps 代表 pseudopotentials）
@@ -852,7 +852,7 @@ V_l(r)=\frac{1}{\phi^\text{ps}_l(r)}[\epsilon^\text{ps}_l-\frac{\hbar^2}{2m}\frac{l(l+1)}{r^2}+\frac{\hbar^2}{2m}\frac{d^2}{dr^2}]\phi^\text{ps}_l(r)，解得。
- 扣除中 Hartree、xc 部分，得到：。
-更多细节见
+更多细节见：www.tcm.phy.cam.ac.uk
<UPF version="2.0.1">
<PP_INFO>
<!-- omitted information here -->
@@ -865,8 +865,8 @@ <!-- -->
从 UPF 文件（注意 UPF 文件也有不同的版本，目前 ABACUS 都支持，若有不支持的，可以提 Github 的 issues 进行讨论）开始，截止到 <PP_HEADER> 之前，提供了赝势文件的作者信息，引用信息以及生成赝势文件所使用的程序和相应输入文件，并附带输入文件参数中的解释。由于此块内容对实际计算并不起作用，因此暂时略过。
-## Section 1:
-<PP_HEADER
+Section 1:
+ <PP_HEADER
generated="Generated using ONCVPSP code by D. R. Hamann" author="Martin Schlipf and Francois Gygi"
date="150105" comment=""
element="Al"
@@ -890,8 +890,8 @@ number_of_proj
="4"/>
<PP_HEADER> 部分尽管已经位于所谓“not human readable”区域，但也并非如此。这部分“标签”（HTML 语境）/block 实际上包含了众多精简过的信息，如元素名称（element）、赝势类型（pseudo_type，模守恒，norm-conserving，NC），相对论效应（relativistic），是否为超软赝势等等信息。当前 Al 理论上其原子序数 13，因此有 13 个电子，但此处 z_valence 参数为 11，即有两个 1s 电子被赝化，只留下 2s, 2p, 3s, 3p 电子共 2+6+2+1 个。对于某些元素，甚至有大核赝势与小核赝势之分，根据赝化电子数量不同进行区分。显而易见地，赝化电子数量越多，则计算量越小，但计算结果的精确程度可能更低。
-## Section 2:
-<PP_MESH>
+Section 2:
+ <PP_MESH>
<PP_R type="real" size=" 602" columns="8">
0.0000 0.0100 0.0200 0.0300 0.0400 0.0500 0.0600 0.0700
<!-- omitted information here -->
@@ -907,8 +907,8 @@ </PP_MESH>
这部分开始出现了关于实空间格点相关量的定义。在 tag 中不仅指定数据类型为实数，也指定当前数据的长度（size），以及数据存储的列数（columns = 8）。PP_R 为格点坐标，PP_RAB 则为格点间距。
-## Section 3:
-<PP_LOCAL type="real" size=" 602" columns="4">
+Section 3:
+ <PP_LOCAL type="real" size=" 602" columns="4">
-4.5793174225E+01 -4.5788454271E+01 -4.5774276797E+01 -4.5750659428E+01
<!-- omitted information here -->
-3.6912752197E+00 -3.6850921941E+00 -3.6789298138E+00 -3.6727880140E+00
@@ -917,8 +917,8 @@ <PP_LOCAL>
部分开始，正式开始写入赝势的具体数值，建立在 <PP_R> 和 <PP_RAB> 所描述的实空间格点上。。<PP_LOCAL> 正是赝势的局域势部分。
-## Section 4:
-<PP_NONLOCAL>
+Section 4:
+ <PP_NONLOCAL>
<PP_BETA.1
type="real"
size=" 602"
@@ -938,8 +938,8 @@ cutoff_radius_index
=" 246" cutoff_radius=" 2.4500000000E+00" >
<!-- omitted information here -->
</PP_BETA.2>
- <PP_BETA.3 type="real" size=" 602" columns="4" index="3" angular_momentum="1"<strong>
-</strong> cutoff_radius_index=" 246" cutoff_radius=" 2.4500000000E+00" >
+ <PP_BETA.3 type="real" size=" 602" columns="4" index="3" angular_momentum="1"
+ cutoff_radius_index=" 246" cutoff_radius=" 2.4500000000E+00" >
<!-- omitted information here -->
</PP_BETA.3>
<PP_BETA.4 type="real" size=" 602" columns="4" index="4" angular_momentum="1"
@@ -956,7 +956,7 @@ \hat{V}^\text{NL}=\sum_{ij}{|\beta_i\rangle D_{ij}\langle\beta_j|}。其中一般被称为非局域势投影子（projector）。
-## Section 5: and
+Section 5: and
<PP_PSWFC>
</PP_PSWFC>
<PP_RHOATOM type="real" size=" 602" columns="4">
@@ -975,7 +975,7 @@ |\beta\rangle和 pswfc 已经乘径向坐标。
-# UnitCell::read_cell_pseudopots()
+UnitCell::read_cell_pseudopots()
link to Github -> link
void UnitCell::read_cell_pseudopots(const std::string &pp_dir, std::ofstream &log)
{
@@ -1030,7 +1030,7 @@ while (ifs.good())
+ while (ifs.good())
{
ifs >> dummy;
if(dummy=="<PP_HEADER>")
@@ -1044,7 +1044,7 @@ if ( ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_MESH>") )
+ if ( ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_MESH>") )
{
read_pseudo_mesh(ifs);
ModuleBase::GlobalFunc::SCAN_END(ifs, "</PP_MESH>");
@@ -1052,7 +1052,7 @@ if (this->nlcc)
+ if (this->nlcc)
{
ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_NLCC>");
read_pseudo_nlcc(ifs);
@@ -1061,12 +1061,12 @@ ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_LOCAL>");
+ ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_LOCAL>");
read_pseudo_local(ifs);
ModuleBase::GlobalFunc::SCAN_END(ifs, "</PP_LOCAL>");
与 类似的还有 , , , 从 则可以读取旋轨耦合相关信息：
-if (has_so)
+ if (has_so)
{
ModuleBase::GlobalFunc::SCAN_BEGIN (ifs,"<PP_ADDINFO>");
read_pseudo_so (ifs);
@@ -1140,7 +1140,7 @@ if(error==0)
+ if(error==0)
{
if(this->atoms[i].flag_empty_element) upf.set_empty_element();
error_ap = upf.average_p(GlobalV::soc_lambda);
@@ -1148,7 +1148,7 @@ if(GlobalV::MY_RANK==0)
+ if(GlobalV::MY_RANK==0)
{
atoms[i].ncpp.set_pseudo_nc( upf );
....
@@ -1178,7 +1178,7 @@ }
该函数属于类 pseudo_nc，而 pseudo_nc 对象为 atom 的数据成员，atoms 则为 UnitCell 的数据成员。pseudo_nc::set_pseudo_h()，pseudo_nc::set_pseudo_atom 和 pseudo_nc::set_pseudo_vl 的内容在此省略，但其分别为将 Hamilton, 原子性质和 Vlocal 相关数据从 upf 对象拷贝。之后(1)使用 lll 刷新为 upf 对象的 projectors 的角动量，然后计算出磁角动量区分时的 projector 个数。(2)取所有 projector 衰减到 0 时候的最大最普适半径。
-# 赝势信息后处理
+赝势信息后处理
回到 module_cell/unitcell.cpp line 663，接下来为每个原子创建目录，在目录中写 [原子label].NONLOCAL 文件。[label].NONLOCAL 文件中内容包含 <HEADER>, <DIJ> 和 <PP_BETA> 三个 tag。
<HEADER> 中包含内容：
ofs << "<HEADER>" << std::endl;
@@ -1222,21 +1222,61 @@ }
ofs << "</PP_BETA>" << std::endl;
-# 赝势信息分发：UnitCell::bcast_unitcell2(void)
+赝势信息分发：UnitCell::bcast_unitcell2(void)
#ifdef __MPI
+接下来对赝势信息进行MPI进程（processor）间的分发：
+#ifdef __MPI
+ bcast_unitcell2();
+#endif
+
+// module_cell/unitcell.cpp:bcast_unitcell2()
+void UnitCell::bcast_unitcell2(void)
+{
+ for (int i = 0; i < ntype; i++)
+ {
+ atoms[i].bcast_atom2();
+ }
+ return;
+}
+
+// module_cell/atom_spec.cpp:Atom::bcast_atom2()
+void Atom::bcast_atom2()
+{
+ this->ncpp.bcast_atom_pseudo();
+}
+
+// module_cell/atom_pseudo.cpp::Atom_pseudo::bcast_atom_pseudo()
+void Atom_pseudo::bcast_atom_pseudo(void)
+{
+....
+ Parallel_Common::bcast_int( lmax );
+....
+ Parallel_Common::bcast_double( etotps );
+....
+ Parallel_Common::bcast_bool( tvanp );
+....
+ Parallel_Common::bcast_string( psd );
+....
+ // below two 'bcast_double' lines of codes seem to have bugs,
+ // on some computers, the code will stuck here for ever.
+ // mohan note 2021-04-28
+ Parallel_Common::bcast_double( dion.c , nbeta * nbeta);
+ Parallel_Common::bcast_double( betar.c, nr * nc );
+}
+
#endif
-# 赝势信息核对
+赝势信息核对
接下来跨原子种类检验泛函是否一致：
-for(int it=0; it<ntype; it++)
+ for(int it=0; it<ntype; it++)
{
if(atoms[0].ncpp.xc_func !=atoms[it].ncpp.xc_func)
{
-# STRU 结构检查：UnitCell::check_structure()
+STRU 结构检查：UnitCell::check_structure()
检验结构中任意两原子之间距离是否大于其固定倍数（<1）的共价半径和，
-check_structure(GlobalV::MIN_DIST_COEF);
+ check_structure(GlobalV::MIN_DIST_COEF);
-# 计算轨道数：UnitCell::cal_natomwfc()
+计算轨道数：UnitCell::cal_natomwfc()
UnitCell::cal_natomwfc() 函数计算所有种类的原子轨道数量加和，对于非 nspin=4，即非 soc（自旋轨道耦合）情况，角量子数 l 和 s 非耦合，l 单独可以作为好的量子数来区分量子态，因此对于每个赝势中定义的 wfc，若其对应 occupation 大于等于 0（即有效 wfc），则对应于其角量子数 l，轨道数量增加 2l+1，即计数其磁量子数 m，也相当于对 alpha 和 beta spin 的单独计数。对于 nspin=4 的情况，若考虑 soc，则轨道数对 j=l+s 的情况，当前原子种类当前角量子数对应轨道数量记为 2l+1+1，否则为 2l+1。对于非 soc 但 nspin=4，当前原子种类轨道当前角量子数对应轨道数量记(2l+1)*2：
void UnitCell::cal_natomwfc(std::ofstream &log)
{
@@ -1291,9 +1331,9 @@ 计算跨原子种类最大角量子数 UnitCell::lmax 和某 l 对应最大 zeta 数 UnitCell::nmax，以及跨原子种类的类内 zeta 数总和最大值 UnitCell::nmax_total
寻找赝势中最大角量子数 UnitCell::lmax_ppwf。
-# 价电子数核对
+价电子数核对
核对赝势中定义的价电子数与 ABACUS 预置库中原子的最小价电子数
-# 获取最大格点数量：UnitCell::cal_meshx()
+获取最大格点数量：UnitCell::cal_meshx()
计算跨原子种类的最大格点数量，存储在 UnitCell::meshx 中，目前 ABACUS 代码中变量命名后缀 x 可能代表 max，正如之前看到 npwx 等。
至此，我们离开函数 UnitCell::read_pseudo()，回到 ModuleESolver::ESolver_FP::Init() 函数。
@@ -1304,7 +1344,7 @@ Introduction to ABACUS: Path to PW calculation - Part 2
下篇：Introduction to ABACUS: Path to PW calculation - Part 4
@@ -1348,7 +1388,7 @@ No results matching "
var gitbook = gitbook || [];
gitbook.push(function() {
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example","attributes":{},"skip":false,"key":"1.2.10.5"}]},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"develop-path3.md","mtime":"2023-10-04T15:11:45.401Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-10-04T15:29:41.868Z"},"basePath":".","book":{"language":""}});
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diff --git a/_book/develop-path4.html b/_book/develop-path4.html
index 1840948c..2b9cddf9 100644
--- a/_book/develop-path4.html
+++ b/_book/develop-path4.html
@@ -750,14 +750,14 @@ Driver
-Driver::atomic_world()
-Driver::driver_run()
-多层继承：Init() functions in esolver class
-Trigger: ESolver_FP::Init()
-平面波格点初始化：PW_Basis:: initgrids()
+Driver
+Driver::atomic_world()
+Driver::driver_run()
+多层继承：Init() functions in esolver class
+Trigger: ESolver_FP::Init()
+平面波格点初始化：PW_Basis:: initgrids()
完成了 INPUT 和 STRU，以及赝势文件的读取环节，接下来我们来到平面波的初始化设置相关部分。
-void ESolver_FP::Init(Input& inp, UnitCell& cell)
+ void ESolver_FP::Init(Input& inp, UnitCell& cell)
{
....
if (inp.nx * inp.ny * inp.nz == 0)
@@ -782,7 +782,7 @@ virtual void initgrids(const double lat0_in,const ModuleBase::Matrix3 latvec_in,
+ virtual void initgrids(const double lat0_in,const ModuleBase::Matrix3 latvec_in,
const double gridecut)
{
// generation of nx, ny and nz are omitted here
@@ -868,7 +868,7 @@ }
❗ 注意：这里还完成了倒空间格点数量 fftnx, fftny 和 fftnz 的赋值。因为 FFT 变换前后的格点数量一般相同，因此 fftnx = nx，fftny = ny，...。
-
+图 1. 然后对平面波在 MPI 进程间进行分发：
//module_esolver/esolver_fp.cpp
void ESolver_FP::Init(Input& inp, UnitCell& cell)
@@ -889,9 +889,9 @@ ::
timer::tick(this->classname, "setuptransform");
}
-PW_Basis::setuptransform()（link）
-# 并行机制简述
-## 并行池
+PW_Basis::setuptransform()（link）
+并行机制简述
+并行池
到这里，我们不得不开始对平面波的 MPI 并行机制有一个大致的认识。在 ABACUS 中，CPU（=processor）首先根据不同的布里渊区 k 点分组被划分成不同的并行池（parallelizaiton pool），每个 pool 都包含几个 k 点，在每个 pool 里面会有完整的对该 k 点求解 Kohn-Sham 方程的过程。因此，在每个 pool 中采用一定数量的 CPU 进程来完成计算。在 INPUT 文件中，KPAR 参数决定了并行池的数量（即 pool 的个数）。换句话说，ABACUS 的 k 点并行机制为，将 k 点（设其数量为 nkpt）分配在 KPAR 个 pool 中，若一共有 nproc 个 processor，则：
- 每个 pool 有
nproc/KPAR 个 processor
@@ -899,7 +899,7 @@ ## MPI 进程编号：rank
+MPI 进程编号：rank
rank 是一个在 MPI 并行里常被用到的变量。在拥有不止一个 processor 的时候，每个 processor 都具有唯一的编号，称为 rank。如果在每个 processor 都有 rank 的基础上还定义了 pool，以及在每个 pool 中的 processor 数量，则 processor 除了有跨 pool 的全局 rank，也可以有 pool 之内的局部 rank，这部分内容见 module_base/global_variable.cpp:
int NPROC = 1;
int KPAR = 1;
@@ -926,7 +926,7 @@ }
}
-## 并行策略
+并行策略
于是问题便到来：在并行条件下，代码究竟是如何执行的？
- 对于多核 CPU，是否运行在其上的所有程序都进行了并行化？
@@ -950,9 +950,9 @@ ## OpenMP-MPI 混合编程
+OpenMP-MPI 混合编程
通常来讲，尽管 OpenMP 提供了线程并行，但由于共享内存可能并不存在于 processors 之间，或 computer, nodes 之间，且没有适合的内存共享系统（multi-socket server），此时如果以 OpenMP 放心运行，则可能得出错误结果或直接报错——因为内存无法访问。对于这种情况，需要使用 MPI（Message passing interface）来维持无内存共享处理单元之间的信息交换，以及信息分发和分布计算，而在处理单元内部，即可以共享内存的域内，则可以通过 OpenMP 技术来进行线程级并行。
-# 实空间格点分发
+实空间格点分发
在简单介绍完并行机制后，我们知道，对于未显式以并行方式实现的函数，其运行将在每一个 processor。在接下来的平面波分发过程中，请始终牢记这一理念，尤其在 processor-local 变量和 processor-global 变量的传值过程中。
稍加回溯：
void ESolver_FP::Init(Input& inp, UnitCell& cell)
@@ -968,7 +968,7 @@ ## 实空间：PW_Basis::distribute_r()
+实空间：PW_Basis::distribute_r()
❗Attention
注意，此时实际调用的也是 PW_Basis_Big 而非 PW_Basis 的 distribute_r() 函数。
@@ -1011,8 +1011,8 @@ {
....
该判断不会 always true。因此 PW_Basis::distribute_r() 将 3D 实空间格点，按照 z 方向进行分发，分给了不同的 processors，并赋值 this->npz，this->nplane, this->startz_current 和 this->nrxx，意义分别为当前 processor 的 z 方向格点数量、xy 平面数量、z 格点的起始索引以及当前 processor 所分得实空间格点总数（分配后 z 方向格点 ×xy 平面格点）。
-
-## 倒空间：PW_Basis::distribute_g()
+图 2. PW_Basis::distribute_r()：设一个pool中有5个processors 倒空间：PW_Basis::distribute_g()
倒空间格点的分发采用了和实空间不同的方式，这主要是因为倒空间“球”的存在（ecutwfc 和 ecutrho），使得非空间中所有点都需要考虑在内，而实空间则并非如此。更一般而言，有限的实空间带来无限的倒空间（即实空间 delta 函数需要无限数量的平面波展开）延展，而有限的倒空间（倒空间 delta 点）带来无限的实空间延展（如一个平面波）。
🔧重构信息
@@ -1066,7 +1066,7 @@
delete
[] st_bottom2D; delete[] st_length2D;
}
-### 分发最小单元：“棍子” - 准备工作
+分发最小单元：“棍子” - 准备工作
穿过布里渊区的整数点（2pi/a 的整数倍）都代表一个三个 index 的平面波，而一系列的点在截断半径以内沿着某个方向就组成了所谓的“stick”（代表平面波集合的“棍子”，一个“棍子”包含了多个平面波，简称就叫“棍子”）。
PW_Basis::count_pw_st() 函数（Link）计算了每个(x,y)对应的“棍子”的底部和“长度”，即对倒空间只分辨(x,y)，则会得到沿 z 方向的点的集合，被称为“棍子”。而“棍子”区域内部每一个点都代表一个平面波。“棍子”的底部对应于最小的 iz 值，“根子”的长度则为当前(x,y)所包含的平面波数量：
for (int ix = ix_start; ix <= ix_end; ++ix)
@@ -1098,7 +1098,7 @@ }
}
-
+图 3. this->count_pw_st(st_length2D, st_bottom2D) 在倒空间分发平面波时，由于 x/y/z 均等在正负半轴 span，因此常常会涉及到 C++ 不支持负数索引的问题（btw: Python 和 FORTRAN 支持负数索引，但支持方式不同），ABACUS 当前所采取的策略是：
if (x<0) x += this->nx; if (y<0) y += this->ny; if (z<0) z += this->nz;
@@ -1107,7 +1107,7 @@ ### “棍子”的分发和分发记录
+“棍子”的分发和分发记录
PW_Basis::collect_st() 和 PW_Basis::divide_sticks_1() 分别排序与分发“棍子”到不同 processor：
- 按照棍子从长到短顺序进行排序，即
st_length2D 由大到小排序，然后适用于 st_bottom2D 等变量
@@ -1136,7 +1136,7 @@ this
->nstnz = this->nst * this->nz;
....
-### 映射表：OOP？
+映射表：OOP？
在倒空间平面波的分发过程中，共建立过四个映射表，分别是 this->fftixy2ip, this->istot2ixy, this->ig2isz 和 this->is2fftixy，其意义分别为：
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diff --git a/_book/develop-path1.html b/_book/develop-path1.html
index 1de92b86..d41c1be3 100644
--- a/_book/develop-path1.html
+++ b/_book/develop-path1.html
@@ -1112,8 +1112,8 @@ <
Input_Conv::Convert()
这个函数实现了从 Input 类对象的数据成员到 GlobalV 和 GlobalC 等全局变量集合的转换。相当于从 Input 到 GlobalV 和 GlobalC，以及其他直接的类的参数上载：
-其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
+其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
void Input_Conv::Convert(void)
{
....
@@ -1308,7 +1308,7 @@
不要忘记我们已经完成 Driver::reading() 函数内容，到达 Driver::atomic_world()。这一点从本文档设置的分级目录中也可以看得到。
-cppvoid Driver::init()
+void Driver::init()
{
this->reading();
this->atomic_world(); // <- here!
@@ -1518,7 +1518,7 @@ 从 SIAB 到 ABACUS（一）：准备工作（施工中 🚧）
下篇：Introduction to ABACUS: Path to PW calculation - Part 2
@@ -1562,7 +1562,7 @@ No results matching "
var gitbook = gitbook || [];
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V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","attributes":{},"skip":false,"key":"1.1.15.5"},{"backlink":"abacus-surface6.html#fig1.1.16.1","level":"1.1.16","list_caption":"Figure: 一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","alt":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","nro":14,"url":"picture/fig_surface6-1.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","attributes":{},"skip":false,"key":"1.1.16.1"},{"backlink":"abacus-surface6.html#fig1.1.16.2","level":"1.1.16","list_caption":"Figure: 静电势（Electrostatic Potential）沿超胞Z轴变化图","alt":"静电势（Electrostatic Potential）沿超胞Z轴变化图","nro":15,"url":"picture/fig_surface6-2.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"静电势（Electrostatic Potential）沿超胞Z轴变化图","attributes":{},"skip":false,"key":"1.1.16.2"},{"backlink":"develop-path4.html#fig1.2.9.1","level":"1.2.9","list_caption":"Figure: ","alt":" 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1)","alt":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","nro":21,"url":"picture/fig_path5-11.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","attributes":{},"skip":false,"key":"1.2.10.3"},{"backlink":"develop-path5.html#fig1.2.10.4","level":"1.2.10","list_caption":"Figure: 1-dimensional example","alt":"1-dimensional example","nro":22,"url":"picture/fig_path5-12.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"1-dimensional example","attributes":{},"skip":false,"key":"1.2.10.4"},{"backlink":"develop-path5.html#fig1.2.10.5","level":"1.2.10","list_caption":"Figure: 2-dimensional example","alt":"2-dimensional example","nro":23,"url":"picture/fig_path5-13.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"2-dimensional example","attributes":{},"skip":false,"key":"1.2.10.5"}]},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"develop-path1.md","mtime":"2023-10-04T14:18:52.079Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-10-04T15:29:41.868Z"},"basePath":".","book":{"language":""}});
});
diff --git a/_book/develop-path2.html b/_book/develop-path2.html
index 191dfe74..d829579b 100644
--- a/_book/develop-path2.html
+++ b/_book/develop-path2.html
@@ -1028,7 +1028,7 @@ // a(i) is lattice vector
}
-我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
+我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
UnitCell::read_atom_positions()
🔧重构思考
@@ -1042,7 +1042,7 @@
::
GlobalFunc::READ_VALUE( ifpos, Coordinate);
STRU 第二行指定坐标类型，被读取为 UnitCell::Coordinate。UnitCell::Coordinate 在 STRU 里有不同选项，⚙ 决定原子的具体位置和单位：
-if(Coordinate != "Cartesian"
+ if(Coordinate != "Cartesian"
&& Coordinate != "Direct"
&& Coordinate != "Cartesian_angstrom"
&& Coordinate != "Cartesian_au"
@@ -1092,7 +1092,7 @@ int na = 0;
+ int na = 0;
this->nat = 0;
assert(ntype>0);
for (int it = 0;it < ntype; it++)
@@ -1105,7 +1105,7 @@ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
bool sequence_match = false;
for(int it2=0; it2<ntype; it2++)
{
@@ -1121,7 +1121,7 @@ }
读取当前原子类型的 starting_magnetization、原子总数 na
-ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
...
ModuleBase::GlobalFunc::READ_VALUE(ifpos, na);
this->atoms[it].na = na;
@@ -1149,17 +1149,17 @@ [
it].m_loc_ = new ModuleBase::Vector3<double>[na];
⚙ 然后在 ATOMIC_POSITIONS 中读取：
-atoms[it].mass = this->atom_mass[it];
+ atoms[it].mass = this->atom_mass[it];
❗ 此处的 atoms[it].mass 与 this->atom_mass[it] 的用法与 atomis[it].label 与 this->atom_label[it] 不同：传值 vs 核对。
接下来读取类中每个原子的速度信息，在做分子动力学模拟的时候可能需要用到：
-for (int ia = 0;ia < na; ia++)
+ for (int ia = 0;ia < na; ia++)
{
ifpos >> v.x >> v.y >> v.z;
然而，当前 STRU 文件在 ATOMIC_POSITIONS 的设计比较复杂，其可以包括任何一组 atom-specific 数据，且数量和顺序均不受限制，这导致判断条件变得复杂，详见 module_cell/read_atoms.cpp:line 536 - 567（link）。
atoms[it].mag 的赋值并非直接读取：
-else if ( tmpid == "mag" || tmpid == "magmom")
+ else if ( tmpid == "mag" || tmpid == "magmom")
{
set_element_mag_zero = true;
double tmpamg=0; ifpos >> tmpamg;
@@ -1185,7 +1185,7 @@ }
⚙ 若 mag/magmom 后有一个值，则读取其值赋给 atoms[it]::mag[ia]，将 input_vec_mag 置为 false，若有三个值，则三个值依次被传入 atoms[it].m_loc_[ia].x, atoms[it].m_loc_[ia].y 和 atoms[it].m_loc_[ia].z，并将 input_vec_mag 置为 true，之后其向量模长为 atoms[it]::mag[ia]，然后在使用 angle1, angle2 来重新生成 mag。
-if(GlobalV::NSPIN==4)
+ if(GlobalV::NSPIN==4)
{
if(GlobalV::NONCOLIN)
{
@@ -1227,7 +1227,7 @@ pw.x input description
ABACUS 对 nspin=4 情况的参数处理：
//module_io/input_conv.cpp line 376
if (INPUT.noncolin || INPUT.lspinorb)
@@ -1312,7 +1312,7 @@
UnitCell::setup_cell(): the rest, and an example of backtracking unclear variable
离开 STRU 文件的解析部分，接下来计算了初始磁化强度：
-//after read STRU, calculate initial total magnetization when NSPIN=2
+ //after read STRU, calculate initial total magnetization when NSPIN=2
if(GlobalV::NSPIN == 2 && !GlobalV::TWO_EFERMI)
{
for(int it = 0;it<this->ntype; it++)
@@ -1326,31 +1326,25 @@ if (std::abs(INPUT.nupdown) > 1e-6)
- {
- GlobalV::TWO_EFERMI = true;
- GlobalV::nupdown = INPUT.nupdown;
- }
-
-因此 GlobalV::TWO_EFERMI 变量实际依赖于 INPUT.nupdown。
-
-- 接下来在
module_io/input.cpp 中寻找含 INPUT.nupdown 的 if(strcmp(...)) 单元，查看在 INPUT 文件中是何参数赋予其具体值：
-
-else if (strcmp("nupdown", word) == 0)
+在 module_io/input_conv.cpp 中寻找该变量，是何变量赋其值，发现： if (std::abs(INPUT.nupdown) > 1e-6)
{
- read_value(ifs, nupdown);
- }
+ GlobalV::TWO_EFERMI = true;
+ GlobalV::nupdown = INPUT.nupdown;
+ }
-即 INPUT.nupdown 在 INPUT 中也为 nupdown。接下来打开 Full keyword list 寻找其解释。
-
+ 因此 GlobalV::TWO_EFERMI 变量实际依赖于 INPUT.nupdown。
+接下来在 module_io/input.cpp 中寻找含 INPUT.nupdown 的 if(strcmp(...)) 单元，查看在 INPUT 文件中是何参数赋予其具体值： else if (strcmp("nupdown", word) == 0)
+ {
+ read_value(ifs, nupdown);
+ }
+
+即 INPUT.nupdown 在 INPUT 中也为 nupdown。接下来打开 Full keyword list 寻找其解释。
得到结果，即 nupdown 为 spin up 和 spin down 电子数量差值：
因此该部分逻辑为：若未使用 nupdown 来指定单电子数量，则对每种原子内每个原子，累加其 mag/magmom，即磁矩模长，赋予 GlobalV::nupdown。❗ 但对于两种方式均赋予，但值不一致的情况未进行处理。
接下来根据在 STRU 中读取的晶胞参数，计算晶胞体积，并计算倒空间矢量（在上篇中已经对 latvec, G, GT, GGT 有所介绍，invGGT 的意义也不言自明）：
-this->omega = std::abs( latvec.Det() ) * this->lat0 * lat0 * lat0 ;
+ this->omega = std::abs( latvec.Det() ) * this->lat0 * lat0 * lat0 ;
this->GT = latvec.Inverse();
this->G = GT.Transpose();
@@ -1442,7 +1436,7 @@ =
static_cast<ModulePW::PW_Basis_Big*>(pw_rho);
对于 ESolver 本身，其指针对象 p_esolver 实际上也有类似操作：
-//Some API to operate E_Solver
+ //Some API to operate E_Solver
void init_esolver(ESolver*& p_esolver)
{
//determine type of esolver based on INPUT information
@@ -1907,7 +1901,7 @@ Introduction to ABACUS: Path to PW calculation - Part 1
下篇：Introduction to ABACUS: Path to PW calculation - Part 3
@@ -1951,7 +1945,7 @@ No results matching "
var gitbook = gitbook || [];
gitbook.push(function() {
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采用PBE交换关联泛函和自旋极化得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出不加电场时，两个自旋方向的能带图几乎一样，都有带隙。","alt":"采用PBE交换关联泛函和自旋极化得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出不加电场时，两个自旋方向的能带图几乎一样，都有带隙。","nro":12,"url":"picture/fig_surface5-4.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"采用PBE交换关联泛函和自旋极化得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出不加电场时，两个自旋方向的能带图几乎一样，都有带隙。","attributes":{},"skip":false,"key":"1.1.15.4"},{"backlink":"abacus-surface5.html#fig1.1.15.5","level":"1.1.15","list_caption":"Figure: 采用PBE交换关联泛函和自旋极化，再给体系加上0.1 V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","alt":"采用PBE交换关联泛函和自旋极化，再给体系加上0.1 V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","nro":13,"url":"picture/fig_surface5-5.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"采用PBE交换关联泛函和自旋极化，再给体系加上0.1 V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","attributes":{},"skip":false,"key":"1.1.15.5"},{"backlink":"abacus-surface6.html#fig1.1.16.1","level":"1.1.16","list_caption":"Figure: 一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","alt":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","nro":14,"url":"picture/fig_surface6-1.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","attributes":{},"skip":false,"key":"1.1.16.1"},{"backlink":"abacus-surface6.html#fig1.1.16.2","level":"1.1.16","list_caption":"Figure: 静电势（Electrostatic Potential）沿超胞Z轴变化图","alt":"静电势（Electrostatic Potential）沿超胞Z轴变化图","nro":15,"url":"picture/fig_surface6-2.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"静电势（Electrostatic Potential）沿超胞Z轴变化图","attributes":{},"skip":false,"key":"1.1.16.2"},{"backlink":"develop-path4.html#fig1.2.9.1","level":"1.2.9","list_caption":"Figure: ","alt":" ","nro":16,"url":"picture/fig_path4-1.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":" ","attributes":{},"skip":false,"key":"1.2.9.1"},{"backlink":"develop-path4.html#fig1.2.9.2","level":"1.2.9","list_caption":"Figure: PW_Basis::distribute_r()：设一个pool中有5个processors","alt":"PW_Basis::distribute_r()：设一个pool中有5个processors","nro":17,"url":"picture/fig_path4-2.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"PW_Basis::distribute_r()：设一个pool中有5个processors","attributes":{},"skip":false,"key":"1.2.9.2"},{"backlink":"develop-path4.html#fig1.2.9.3","level":"1.2.9","list_caption":"Figure: this->count_pw_st(st_length2D, st_bottom2D)","alt":"this->count_pw_st(st_length2D, st_bottom2D)","nro":18,"url":"picture/fig_path4-3.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"this->count_pw_st(st_length2D, st_bottom2D)","attributes":{},"skip":false,"key":"1.2.9.3"},{"backlink":"develop-path5.html#fig1.2.10.1","level":"1.2.10","list_caption":"Figure: 善用Ctrl+F","alt":"善用Ctrl+F","nro":19,"url":"picture/fig_path5-9.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"善用Ctrl+F","attributes":{},"skip":false,"key":"1.2.10.1"},{"backlink":"develop-path5.html#fig1.2.10.2","level":"1.2.10","list_caption":"Figure: klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","alt":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","nro":20,"url":"picture/fig_path5-10.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","attributes":{},"skip":false,"key":"1.2.10.2"},{"backlink":"develop-path5.html#fig1.2.10.3","level":"1.2.10","list_caption":"Figure: klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","alt":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","nro":21,"url":"picture/fig_path5-11.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","attributes":{},"skip":false,"key":"1.2.10.3"},{"backlink":"develop-path5.html#fig1.2.10.4","level":"1.2.10","list_caption":"Figure: 1-dimensional example","alt":"1-dimensional example","nro":22,"url":"picture/fig_path5-12.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"1-dimensional example","attributes":{},"skip":false,"key":"1.2.10.4"},{"backlink":"develop-path5.html#fig1.2.10.5","level":"1.2.10","list_caption":"Figure: 2-dimensional example","alt":"2-dimensional example","nro":23,"url":"picture/fig_path5-13.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"2-dimensional example","attributes":{},"skip":false,"key":"1.2.10.5"}]},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"develop-path2.md","mtime":"2023-10-04T14:37:12.149Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-10-04T15:29:41.868Z"},"basePath":".","book":{"language":""}});
});
diff --git a/_book/develop-path3.html b/_book/develop-path3.html
index b8de33d9..09176394 100644
--- a/_book/develop-path3.html
+++ b/_book/develop-path3.html
@@ -750,11 +750,11 @@ Driver
-Driver::atomic_world()
-Driver::driver_run()
-多层继承：Init() functions in esolver class
-Trigger: ESolver_FP::Init()
+Driver
+Driver::atomic_world()
+Driver::driver_run()
+多层继承：Init() functions in esolver class
+Trigger: ESolver_FP::Init()
承接上篇中已经导入的结构信息，以及了解到构造函数及其伴随的变量初始化和 ABACUS 里应用到的 C++ 多态编程，接下来即将（逐渐）步入 ABACUS 的核心内容。我们暂时跳过位于 source/driver_run.cpp:driver_run() 的：
// 3. For these two types of calculations
// nothing else need to be initialized
@@ -830,14 +830,14 @@ }
同理，ESolver_KS 的数据成员，也被 ESolver_KS_PW 继承。ESolver_FP::Init() 首先调用 UnitCell::read_pseudo() 函数进行赝势文件读取，而将赝势文件读取任务放在 FP 层级下，也暗示对于 ABACUS 的第一性原理方法实现来讲，都需要使用赝势。
-Pseudopotential import: UnitCell::read_pseudo()
+Pseudopotential import: UnitCell::read_pseudo()
void UnitCell::read_pseudo(std::ofstream &ofs)
{
read_cell_pseudopots(GlobalV::global_pseudo_dir, ofs);
在解读赝势文件读取功能之前，首先需要对赝势文件的结构和信息做一定程度的了解。
-# ONCV pseudopotential file
-## Section 0: Norm-conserving conditions, generation of pseudopotential and header of exact UPF file
+ONCV pseudopotential file
+Section 0: Norm-conserving conditions, generation of pseudopotential and header of exact UPF file
赝势的意义不言自明，其中模守恒赝势需满足如下条件：
- （赝势得到的能级和全电子方法求解的能级一样，这里 ps 代表 pseudopotentials）
@@ -852,7 +852,7 @@ V_l(r)=\frac{1}{\phi^\text{ps}_l(r)}[\epsilon^\text{ps}_l-\frac{\hbar^2}{2m}\frac{l(l+1)}{r^2}+\frac{\hbar^2}{2m}\frac{d^2}{dr^2}]\phi^\text{ps}_l(r)，解得。
- 扣除中 Hartree、xc 部分，得到：。
-更多细节见
+更多细节见：www.tcm.phy.cam.ac.uk
<UPF version="2.0.1">
<PP_INFO>
<!-- omitted information here -->
@@ -865,8 +865,8 @@ <!-- -->
从 UPF 文件（注意 UPF 文件也有不同的版本，目前 ABACUS 都支持，若有不支持的，可以提 Github 的 issues 进行讨论）开始，截止到 <PP_HEADER> 之前，提供了赝势文件的作者信息，引用信息以及生成赝势文件所使用的程序和相应输入文件，并附带输入文件参数中的解释。由于此块内容对实际计算并不起作用，因此暂时略过。
-## Section 1:
-<PP_HEADER
+Section 1:
+ <PP_HEADER
generated="Generated using ONCVPSP code by D. R. Hamann" author="Martin Schlipf and Francois Gygi"
date="150105" comment=""
element="Al"
@@ -890,8 +890,8 @@ number_of_proj
="4"/>
<PP_HEADER> 部分尽管已经位于所谓“not human readable”区域，但也并非如此。这部分“标签”（HTML 语境）/block 实际上包含了众多精简过的信息，如元素名称（element）、赝势类型（pseudo_type，模守恒，norm-conserving，NC），相对论效应（relativistic），是否为超软赝势等等信息。当前 Al 理论上其原子序数 13，因此有 13 个电子，但此处 z_valence 参数为 11，即有两个 1s 电子被赝化，只留下 2s, 2p, 3s, 3p 电子共 2+6+2+1 个。对于某些元素，甚至有大核赝势与小核赝势之分，根据赝化电子数量不同进行区分。显而易见地，赝化电子数量越多，则计算量越小，但计算结果的精确程度可能更低。
-## Section 2:
-<PP_MESH>
+Section 2:
+ <PP_MESH>
<PP_R type="real" size=" 602" columns="8">
0.0000 0.0100 0.0200 0.0300 0.0400 0.0500 0.0600 0.0700
<!-- omitted information here -->
@@ -907,8 +907,8 @@ </PP_MESH>
这部分开始出现了关于实空间格点相关量的定义。在 tag 中不仅指定数据类型为实数，也指定当前数据的长度（size），以及数据存储的列数（columns = 8）。PP_R 为格点坐标，PP_RAB 则为格点间距。
-## Section 3:
-<PP_LOCAL type="real" size=" 602" columns="4">
+Section 3:
+ <PP_LOCAL type="real" size=" 602" columns="4">
-4.5793174225E+01 -4.5788454271E+01 -4.5774276797E+01 -4.5750659428E+01
<!-- omitted information here -->
-3.6912752197E+00 -3.6850921941E+00 -3.6789298138E+00 -3.6727880140E+00
@@ -917,8 +917,8 @@ <PP_LOCAL>
部分开始，正式开始写入赝势的具体数值，建立在 <PP_R> 和 <PP_RAB> 所描述的实空间格点上。。<PP_LOCAL> 正是赝势的局域势部分。
-## Section 4:
-<PP_NONLOCAL>
+Section 4:
+ <PP_NONLOCAL>
<PP_BETA.1
type="real"
size=" 602"
@@ -938,8 +938,8 @@ cutoff_radius_index
=" 246" cutoff_radius=" 2.4500000000E+00" >
<!-- omitted information here -->
</PP_BETA.2>
- <PP_BETA.3 type="real" size=" 602" columns="4" index="3" angular_momentum="1"<strong>
-</strong> cutoff_radius_index=" 246" cutoff_radius=" 2.4500000000E+00" >
+ <PP_BETA.3 type="real" size=" 602" columns="4" index="3" angular_momentum="1"
+ cutoff_radius_index=" 246" cutoff_radius=" 2.4500000000E+00" >
<!-- omitted information here -->
</PP_BETA.3>
<PP_BETA.4 type="real" size=" 602" columns="4" index="4" angular_momentum="1"
@@ -956,7 +956,7 @@ \hat{V}^\text{NL}=\sum_{ij}{|\beta_i\rangle D_{ij}\langle\beta_j|}。其中一般被称为非局域势投影子（projector）。
-## Section 5: and
+Section 5: and
<PP_PSWFC>
</PP_PSWFC>
<PP_RHOATOM type="real" size=" 602" columns="4">
@@ -975,7 +975,7 @@ |\beta\rangle和 pswfc 已经乘径向坐标。
-# UnitCell::read_cell_pseudopots()
+UnitCell::read_cell_pseudopots()
link to Github -> link
void UnitCell::read_cell_pseudopots(const std::string &pp_dir, std::ofstream &log)
{
@@ -1030,7 +1030,7 @@ while (ifs.good())
+ while (ifs.good())
{
ifs >> dummy;
if(dummy=="<PP_HEADER>")
@@ -1044,7 +1044,7 @@ if ( ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_MESH>") )
+ if ( ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_MESH>") )
{
read_pseudo_mesh(ifs);
ModuleBase::GlobalFunc::SCAN_END(ifs, "</PP_MESH>");
@@ -1052,7 +1052,7 @@ if (this->nlcc)
+ if (this->nlcc)
{
ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_NLCC>");
read_pseudo_nlcc(ifs);
@@ -1061,12 +1061,12 @@ ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_LOCAL>");
+ ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_LOCAL>");
read_pseudo_local(ifs);
ModuleBase::GlobalFunc::SCAN_END(ifs, "</PP_LOCAL>");
与 类似的还有 , , , 从 则可以读取旋轨耦合相关信息：
-if (has_so)
+ if (has_so)
{
ModuleBase::GlobalFunc::SCAN_BEGIN (ifs,"<PP_ADDINFO>");
read_pseudo_so (ifs);
@@ -1140,7 +1140,7 @@ if(error==0)
+ if(error==0)
{
if(this->atoms[i].flag_empty_element) upf.set_empty_element();
error_ap = upf.average_p(GlobalV::soc_lambda);
@@ -1148,7 +1148,7 @@ if(GlobalV::MY_RANK==0)
+ if(GlobalV::MY_RANK==0)
{
atoms[i].ncpp.set_pseudo_nc( upf );
....
@@ -1178,7 +1178,7 @@ }
该函数属于类 pseudo_nc，而 pseudo_nc 对象为 atom 的数据成员，atoms 则为 UnitCell 的数据成员。pseudo_nc::set_pseudo_h()，pseudo_nc::set_pseudo_atom 和 pseudo_nc::set_pseudo_vl 的内容在此省略，但其分别为将 Hamilton, 原子性质和 Vlocal 相关数据从 upf 对象拷贝。之后(1)使用 lll 刷新为 upf 对象的 projectors 的角动量，然后计算出磁角动量区分时的 projector 个数。(2)取所有 projector 衰减到 0 时候的最大最普适半径。
-# 赝势信息后处理
+赝势信息后处理
回到 module_cell/unitcell.cpp line 663，接下来为每个原子创建目录，在目录中写 [原子label].NONLOCAL 文件。[label].NONLOCAL 文件中内容包含 <HEADER>, <DIJ> 和 <PP_BETA> 三个 tag。
<HEADER> 中包含内容：
ofs << "<HEADER>" << std::endl;
@@ -1222,21 +1222,61 @@ }
ofs << "</PP_BETA>" << std::endl;
-# 赝势信息分发：UnitCell::bcast_unitcell2(void)
+赝势信息分发：UnitCell::bcast_unitcell2(void)
#ifdef __MPI
+接下来对赝势信息进行MPI进程（processor）间的分发：
+#ifdef __MPI
+ bcast_unitcell2();
+#endif
+
+// module_cell/unitcell.cpp:bcast_unitcell2()
+void UnitCell::bcast_unitcell2(void)
+{
+ for (int i = 0; i < ntype; i++)
+ {
+ atoms[i].bcast_atom2();
+ }
+ return;
+}
+
+// module_cell/atom_spec.cpp:Atom::bcast_atom2()
+void Atom::bcast_atom2()
+{
+ this->ncpp.bcast_atom_pseudo();
+}
+
+// module_cell/atom_pseudo.cpp::Atom_pseudo::bcast_atom_pseudo()
+void Atom_pseudo::bcast_atom_pseudo(void)
+{
+....
+ Parallel_Common::bcast_int( lmax );
+....
+ Parallel_Common::bcast_double( etotps );
+....
+ Parallel_Common::bcast_bool( tvanp );
+....
+ Parallel_Common::bcast_string( psd );
+....
+ // below two 'bcast_double' lines of codes seem to have bugs,
+ // on some computers, the code will stuck here for ever.
+ // mohan note 2021-04-28
+ Parallel_Common::bcast_double( dion.c , nbeta * nbeta);
+ Parallel_Common::bcast_double( betar.c, nr * nc );
+}
+
#endif
-# 赝势信息核对
+赝势信息核对
接下来跨原子种类检验泛函是否一致：
-for(int it=0; it<ntype; it++)
+ for(int it=0; it<ntype; it++)
{
if(atoms[0].ncpp.xc_func !=atoms[it].ncpp.xc_func)
{
-# STRU 结构检查：UnitCell::check_structure()
+STRU 结构检查：UnitCell::check_structure()
检验结构中任意两原子之间距离是否大于其固定倍数（<1）的共价半径和，
-check_structure(GlobalV::MIN_DIST_COEF);
+ check_structure(GlobalV::MIN_DIST_COEF);
-# 计算轨道数：UnitCell::cal_natomwfc()
+计算轨道数：UnitCell::cal_natomwfc()
UnitCell::cal_natomwfc() 函数计算所有种类的原子轨道数量加和，对于非 nspin=4，即非 soc（自旋轨道耦合）情况，角量子数 l 和 s 非耦合，l 单独可以作为好的量子数来区分量子态，因此对于每个赝势中定义的 wfc，若其对应 occupation 大于等于 0（即有效 wfc），则对应于其角量子数 l，轨道数量增加 2l+1，即计数其磁量子数 m，也相当于对 alpha 和 beta spin 的单独计数。对于 nspin=4 的情况，若考虑 soc，则轨道数对 j=l+s 的情况，当前原子种类当前角量子数对应轨道数量记为 2l+1+1，否则为 2l+1。对于非 soc 但 nspin=4，当前原子种类轨道当前角量子数对应轨道数量记(2l+1)*2：
void UnitCell::cal_natomwfc(std::ofstream &log)
{
@@ -1291,9 +1331,9 @@ 计算跨原子种类最大角量子数 UnitCell::lmax 和某 l 对应最大 zeta 数 UnitCell::nmax，以及跨原子种类的类内 zeta 数总和最大值 UnitCell::nmax_total
寻找赝势中最大角量子数 UnitCell::lmax_ppwf。
-# 价电子数核对
+价电子数核对
核对赝势中定义的价电子数与 ABACUS 预置库中原子的最小价电子数
-# 获取最大格点数量：UnitCell::cal_meshx()
+获取最大格点数量：UnitCell::cal_meshx()
计算跨原子种类的最大格点数量，存储在 UnitCell::meshx 中，目前 ABACUS 代码中变量命名后缀 x 可能代表 max，正如之前看到 npwx 等。
至此，我们离开函数 UnitCell::read_pseudo()，回到 ModuleESolver::ESolver_FP::Init() 函数。
@@ -1304,7 +1344,7 @@ Introduction to ABACUS: Path to PW calculation - Part 2
下篇：Introduction to ABACUS: Path to PW calculation - Part 4
@@ -1348,7 +1388,7 @@ No results matching "
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采用PBE交换关联泛函和自旋极化得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出不加电场时，两个自旋方向的能带图几乎一样，都有带隙。","alt":"采用PBE交换关联泛函和自旋极化得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出不加电场时，两个自旋方向的能带图几乎一样，都有带隙。","nro":12,"url":"picture/fig_surface5-4.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"采用PBE交换关联泛函和自旋极化得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出不加电场时，两个自旋方向的能带图几乎一样，都有带隙。","attributes":{},"skip":false,"key":"1.1.15.4"},{"backlink":"abacus-surface5.html#fig1.1.15.5","level":"1.1.15","list_caption":"Figure: 采用PBE交换关联泛函和自旋极化，再给体系加上0.1 V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","alt":"采用PBE交换关联泛函和自旋极化，再给体系加上0.1 V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","nro":13,"url":"picture/fig_surface5-5.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"采用PBE交换关联泛函和自旋极化，再给体系加上0.1 V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","attributes":{},"skip":false,"key":"1.1.15.5"},{"backlink":"abacus-surface6.html#fig1.1.16.1","level":"1.1.16","list_caption":"Figure: 一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","alt":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","nro":14,"url":"picture/fig_surface6-1.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","attributes":{},"skip":false,"key":"1.1.16.1"},{"backlink":"abacus-surface6.html#fig1.1.16.2","level":"1.1.16","list_caption":"Figure: 静电势（Electrostatic Potential）沿超胞Z轴变化图","alt":"静电势（Electrostatic Potential）沿超胞Z轴变化图","nro":15,"url":"picture/fig_surface6-2.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"静电势（Electrostatic Potential）沿超胞Z轴变化图","attributes":{},"skip":false,"key":"1.1.16.2"},{"backlink":"develop-path4.html#fig1.2.9.1","level":"1.2.9","list_caption":"Figure: ","alt":" ","nro":16,"url":"picture/fig_path4-1.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":" ","attributes":{},"skip":false,"key":"1.2.9.1"},{"backlink":"develop-path4.html#fig1.2.9.2","level":"1.2.9","list_caption":"Figure: PW_Basis::distribute_r()：设一个pool中有5个processors","alt":"PW_Basis::distribute_r()：设一个pool中有5个processors","nro":17,"url":"picture/fig_path4-2.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"PW_Basis::distribute_r()：设一个pool中有5个processors","attributes":{},"skip":false,"key":"1.2.9.2"},{"backlink":"develop-path4.html#fig1.2.9.3","level":"1.2.9","list_caption":"Figure: this->count_pw_st(st_length2D, st_bottom2D)","alt":"this->count_pw_st(st_length2D, st_bottom2D)","nro":18,"url":"picture/fig_path4-3.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"this->count_pw_st(st_length2D, st_bottom2D)","attributes":{},"skip":false,"key":"1.2.9.3"},{"backlink":"develop-path5.html#fig1.2.10.1","level":"1.2.10","list_caption":"Figure: 善用Ctrl+F","alt":"善用Ctrl+F","nro":19,"url":"picture/fig_path5-9.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"善用Ctrl+F","attributes":{},"skip":false,"key":"1.2.10.1"},{"backlink":"develop-path5.html#fig1.2.10.2","level":"1.2.10","list_caption":"Figure: klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","alt":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","nro":20,"url":"picture/fig_path5-10.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","attributes":{},"skip":false,"key":"1.2.10.2"},{"backlink":"develop-path5.html#fig1.2.10.3","level":"1.2.10","list_caption":"Figure: klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","alt":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","nro":21,"url":"picture/fig_path5-11.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","attributes":{},"skip":false,"key":"1.2.10.3"},{"backlink":"develop-path5.html#fig1.2.10.4","level":"1.2.10","list_caption":"Figure: 1-dimensional example","alt":"1-dimensional example","nro":22,"url":"picture/fig_path5-12.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"1-dimensional example","attributes":{},"skip":false,"key":"1.2.10.4"},{"backlink":"develop-path5.html#fig1.2.10.5","level":"1.2.10","list_caption":"Figure: 2-dimensional example","alt":"2-dimensional example","nro":23,"url":"picture/fig_path5-13.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"2-dimensional example","attributes":{},"skip":false,"key":"1.2.10.5"}]},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"develop-path3.md","mtime":"2023-10-04T15:11:45.401Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-10-04T15:29:41.868Z"},"basePath":".","book":{"language":""}});
});
diff --git a/_book/develop-path4.html b/_book/develop-path4.html
index 1840948c..2b9cddf9 100644
--- a/_book/develop-path4.html
+++ b/_book/develop-path4.html
@@ -750,14 +750,14 @@ Driver
-Driver::atomic_world()
-Driver::driver_run()
-多层继承：Init() functions in esolver class
-Trigger: ESolver_FP::Init()
-平面波格点初始化：PW_Basis:: initgrids()
+Driver
+Driver::atomic_world()
+Driver::driver_run()
+多层继承：Init() functions in esolver class
+Trigger: ESolver_FP::Init()
+平面波格点初始化：PW_Basis:: initgrids()
完成了 INPUT 和 STRU，以及赝势文件的读取环节，接下来我们来到平面波的初始化设置相关部分。
-void ESolver_FP::Init(Input& inp, UnitCell& cell)
+ void ESolver_FP::Init(Input& inp, UnitCell& cell)
{
....
if (inp.nx * inp.ny * inp.nz == 0)
@@ -782,7 +782,7 @@ virtual void initgrids(const double lat0_in,const ModuleBase::Matrix3 latvec_in,
+ virtual void initgrids(const double lat0_in,const ModuleBase::Matrix3 latvec_in,
const double gridecut)
{
// generation of nx, ny and nz are omitted here
@@ -868,7 +868,7 @@ }
❗ 注意：这里还完成了倒空间格点数量 fftnx, fftny 和 fftnz 的赋值。因为 FFT 变换前后的格点数量一般相同，因此 fftnx = nx，fftny = ny，...。
-
+图 1. 然后对平面波在 MPI 进程间进行分发：
//module_esolver/esolver_fp.cpp
void ESolver_FP::Init(Input& inp, UnitCell& cell)
@@ -889,9 +889,9 @@ ::
timer::tick(this->classname, "setuptransform");
}
-PW_Basis::setuptransform()（link）
-# 并行机制简述
-## 并行池
+PW_Basis::setuptransform()（link）
+并行机制简述
+并行池
到这里，我们不得不开始对平面波的 MPI 并行机制有一个大致的认识。在 ABACUS 中，CPU（=processor）首先根据不同的布里渊区 k 点分组被划分成不同的并行池（parallelizaiton pool），每个 pool 都包含几个 k 点，在每个 pool 里面会有完整的对该 k 点求解 Kohn-Sham 方程的过程。因此，在每个 pool 中采用一定数量的 CPU 进程来完成计算。在 INPUT 文件中，KPAR 参数决定了并行池的数量（即 pool 的个数）。换句话说，ABACUS 的 k 点并行机制为，将 k 点（设其数量为 nkpt）分配在 KPAR 个 pool 中，若一共有 nproc 个 processor，则：
- 每个 pool 有
nproc/KPAR 个 processor
@@ -899,7 +899,7 @@ ## MPI 进程编号：rank
+MPI 进程编号：rank
rank 是一个在 MPI 并行里常被用到的变量。在拥有不止一个 processor 的时候，每个 processor 都具有唯一的编号，称为 rank。如果在每个 processor 都有 rank 的基础上还定义了 pool，以及在每个 pool 中的 processor 数量，则 processor 除了有跨 pool 的全局 rank，也可以有 pool 之内的局部 rank，这部分内容见 module_base/global_variable.cpp:
int NPROC = 1;
int KPAR = 1;
@@ -926,7 +926,7 @@ }
}
-## 并行策略
+并行策略
于是问题便到来：在并行条件下，代码究竟是如何执行的？
- 对于多核 CPU，是否运行在其上的所有程序都进行了并行化？
@@ -950,9 +950,9 @@ ## OpenMP-MPI 混合编程
+OpenMP-MPI 混合编程
通常来讲，尽管 OpenMP 提供了线程并行，但由于共享内存可能并不存在于 processors 之间，或 computer, nodes 之间，且没有适合的内存共享系统（multi-socket server），此时如果以 OpenMP 放心运行，则可能得出错误结果或直接报错——因为内存无法访问。对于这种情况，需要使用 MPI（Message passing interface）来维持无内存共享处理单元之间的信息交换，以及信息分发和分布计算，而在处理单元内部，即可以共享内存的域内，则可以通过 OpenMP 技术来进行线程级并行。
-# 实空间格点分发
+实空间格点分发
在简单介绍完并行机制后，我们知道，对于未显式以并行方式实现的函数，其运行将在每一个 processor。在接下来的平面波分发过程中，请始终牢记这一理念，尤其在 processor-local 变量和 processor-global 变量的传值过程中。
稍加回溯：
void ESolver_FP::Init(Input& inp, UnitCell& cell)
@@ -968,7 +968,7 @@ ## 实空间：PW_Basis::distribute_r()
+实空间：PW_Basis::distribute_r()
❗Attention
注意，此时实际调用的也是 PW_Basis_Big 而非 PW_Basis 的 distribute_r() 函数。
@@ -1011,8 +1011,8 @@ {
....
该判断不会 always true。因此 PW_Basis::distribute_r() 将 3D 实空间格点，按照 z 方向进行分发，分给了不同的 processors，并赋值 this->npz，this->nplane, this->startz_current 和 this->nrxx，意义分别为当前 processor 的 z 方向格点数量、xy 平面数量、z 格点的起始索引以及当前 processor 所分得实空间格点总数（分配后 z 方向格点 ×xy 平面格点）。
-
-## 倒空间：PW_Basis::distribute_g()
+图 2. PW_Basis::distribute_r()：设一个pool中有5个processors 倒空间：PW_Basis::distribute_g()
倒空间格点的分发采用了和实空间不同的方式，这主要是因为倒空间“球”的存在（ecutwfc 和 ecutrho），使得非空间中所有点都需要考虑在内，而实空间则并非如此。更一般而言，有限的实空间带来无限的倒空间（即实空间 delta 函数需要无限数量的平面波展开）延展，而有限的倒空间（倒空间 delta 点）带来无限的实空间延展（如一个平面波）。
🔧重构信息
@@ -1066,7 +1066,7 @@
delete
[] st_bottom2D; delete[] st_length2D;
}
-### 分发最小单元：“棍子” - 准备工作
+分发最小单元：“棍子” - 准备工作
穿过布里渊区的整数点（2pi/a 的整数倍）都代表一个三个 index 的平面波，而一系列的点在截断半径以内沿着某个方向就组成了所谓的“stick”（代表平面波集合的“棍子”，一个“棍子”包含了多个平面波，简称就叫“棍子”）。
PW_Basis::count_pw_st() 函数（Link）计算了每个(x,y)对应的“棍子”的底部和“长度”，即对倒空间只分辨(x,y)，则会得到沿 z 方向的点的集合，被称为“棍子”。而“棍子”区域内部每一个点都代表一个平面波。“棍子”的底部对应于最小的 iz 值，“根子”的长度则为当前(x,y)所包含的平面波数量：
for (int ix = ix_start; ix <= ix_end; ++ix)
@@ -1098,7 +1098,7 @@ }
}
-
+图 3. this->count_pw_st(st_length2D, st_bottom2D) 在倒空间分发平面波时，由于 x/y/z 均等在正负半轴 span，因此常常会涉及到 C++ 不支持负数索引的问题（btw: Python 和 FORTRAN 支持负数索引，但支持方式不同），ABACUS 当前所采取的策略是：
if (x<0) x += this->nx; if (y<0) y += this->ny; if (z<0) z += this->nz;
@@ -1107,7 +1107,7 @@ ### “棍子”的分发和分发记录
+“棍子”的分发和分发记录
PW_Basis::collect_st() 和 PW_Basis::divide_sticks_1() 分别排序与分发“棍子”到不同 processor：
- 按照棍子从长到短顺序进行排序，即
st_length2D 由大到小排序，然后适用于 st_bottom2D 等变量
@@ -1136,7 +1136,7 @@ this
->nstnz = this->nst * this->nz;
....
-### 映射表：OOP？
+映射表：OOP？
在倒空间平面波的分发过程中，共建立过四个映射表，分别是 this->fftixy2ip, this->istot2ixy, this->ig2isz 和 this->is2fftixy，其意义分别为：
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diff --git a/_book/develop-path1.html b/_book/develop-path1.html
index 1de92b86..d41c1be3 100644
--- a/_book/develop-path1.html
+++ b/_book/develop-path1.html
@@ -1112,8 +1112,8 @@ <
Input_Conv::Convert()
这个函数实现了从 Input 类对象的数据成员到 GlobalV 和 GlobalC 等全局变量集合的转换。相当于从 Input 到 GlobalV 和 GlobalC，以及其他直接的类的参数上载：
-其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
+其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
void Input_Conv::Convert(void)
{
....
@@ -1308,7 +1308,7 @@
不要忘记我们已经完成 Driver::reading() 函数内容，到达 Driver::atomic_world()。这一点从本文档设置的分级目录中也可以看得到。
-cppvoid Driver::init()
+void Driver::init()
{
this->reading();
this->atomic_world(); // <- here!
@@ -1518,7 +1518,7 @@ 从 SIAB 到 ABACUS（一）：准备工作（施工中 🚧）
下篇：Introduction to ABACUS: Path to PW calculation - Part 2
@@ -1562,7 +1562,7 @@ No results matching "
var gitbook = gitbook || [];
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index 191dfe74..d829579b 100644
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@@ -1028,7 +1028,7 @@ // a(i) is lattice vector
}
-我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
+我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
UnitCell::read_atom_positions()
🔧重构思考
@@ -1042,7 +1042,7 @@
::
GlobalFunc::READ_VALUE( ifpos, Coordinate);
STRU 第二行指定坐标类型，被读取为 UnitCell::Coordinate。UnitCell::Coordinate 在 STRU 里有不同选项，⚙ 决定原子的具体位置和单位：
-if(Coordinate != "Cartesian"
+ if(Coordinate != "Cartesian"
&& Coordinate != "Direct"
&& Coordinate != "Cartesian_angstrom"
&& Coordinate != "Cartesian_au"
@@ -1092,7 +1092,7 @@ int na = 0;
+ int na = 0;
this->nat = 0;
assert(ntype>0);
for (int it = 0;it < ntype; it++)
@@ -1105,7 +1105,7 @@ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
bool sequence_match = false;
for(int it2=0; it2<ntype; it2++)
{
@@ -1121,7 +1121,7 @@ }
读取当前原子类型的 starting_magnetization、原子总数 na
-ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
...
ModuleBase::GlobalFunc::READ_VALUE(ifpos, na);
this->atoms[it].na = na;
@@ -1149,17 +1149,17 @@ [
it].m_loc_ = new ModuleBase::Vector3<double>[na];
⚙ 然后在 ATOMIC_POSITIONS 中读取：
-atoms[it].mass = this->atom_mass[it];
+ atoms[it].mass = this->atom_mass[it];
❗ 此处的 atoms[it].mass 与 this->atom_mass[it] 的用法与 atomis[it].label 与 this->atom_label[it] 不同：传值 vs 核对。
接下来读取类中每个原子的速度信息，在做分子动力学模拟的时候可能需要用到：
-for (int ia = 0;ia < na; ia++)
+ for (int ia = 0;ia < na; ia++)
{
ifpos >> v.x >> v.y >> v.z;
然而，当前 STRU 文件在 ATOMIC_POSITIONS 的设计比较复杂，其可以包括任何一组 atom-specific 数据，且数量和顺序均不受限制，这导致判断条件变得复杂，详见 module_cell/read_atoms.cpp:line 536 - 567（link）。
atoms[it].mag 的赋值并非直接读取：
-else if ( tmpid == "mag" || tmpid == "magmom")
+ else if ( tmpid == "mag" || tmpid == "magmom")
{
set_element_mag_zero = true;
double tmpamg=0; ifpos >> tmpamg;
@@ -1185,7 +1185,7 @@ }
⚙ 若 mag/magmom 后有一个值，则读取其值赋给 atoms[it]::mag[ia]，将 input_vec_mag 置为 false，若有三个值，则三个值依次被传入 atoms[it].m_loc_[ia].x, atoms[it].m_loc_[ia].y 和 atoms[it].m_loc_[ia].z，并将 input_vec_mag 置为 true，之后其向量模长为 atoms[it]::mag[ia]，然后在使用 angle1, angle2 来重新生成 mag。
-if(GlobalV::NSPIN==4)
+ if(GlobalV::NSPIN==4)
{
if(GlobalV::NONCOLIN)
{
@@ -1227,7 +1227,7 @@ pw.x input description
ABACUS 对 nspin=4 情况的参数处理：
//module_io/input_conv.cpp line 376
if (INPUT.noncolin || INPUT.lspinorb)
@@ -1312,7 +1312,7 @@
UnitCell::setup_cell(): the rest, and an example of backtracking unclear variable
离开 STRU 文件的解析部分，接下来计算了初始磁化强度：
-//after read STRU, calculate initial total magnetization when NSPIN=2
+ //after read STRU, calculate initial total magnetization when NSPIN=2
if(GlobalV::NSPIN == 2 && !GlobalV::TWO_EFERMI)
{
for(int it = 0;it<this->ntype; it++)
@@ -1326,31 +1326,25 @@ if (std::abs(INPUT.nupdown) > 1e-6)
- {
- GlobalV::TWO_EFERMI = true;
- GlobalV::nupdown = INPUT.nupdown;
- }
-
-因此 GlobalV::TWO_EFERMI 变量实际依赖于 INPUT.nupdown。
-
-- 接下来在
module_io/input.cpp 中寻找含 INPUT.nupdown 的 if(strcmp(...)) 单元，查看在 INPUT 文件中是何参数赋予其具体值：
-
-else if (strcmp("nupdown", word) == 0)
+在 module_io/input_conv.cpp 中寻找该变量，是何变量赋其值，发现： if (std::abs(INPUT.nupdown) > 1e-6)
{
- read_value(ifs, nupdown);
- }
+ GlobalV::TWO_EFERMI = true;
+ GlobalV::nupdown = INPUT.nupdown;
+ }
-即 INPUT.nupdown 在 INPUT 中也为 nupdown。接下来打开 Full keyword list 寻找其解释。
-
+ 因此 GlobalV::TWO_EFERMI 变量实际依赖于 INPUT.nupdown。
+接下来在 module_io/input.cpp 中寻找含 INPUT.nupdown 的 if(strcmp(...)) 单元，查看在 INPUT 文件中是何参数赋予其具体值： else if (strcmp("nupdown", word) == 0)
+ {
+ read_value(ifs, nupdown);
+ }
+
+即 INPUT.nupdown 在 INPUT 中也为 nupdown。接下来打开 Full keyword list 寻找其解释。
得到结果，即 nupdown 为 spin up 和 spin down 电子数量差值：
因此该部分逻辑为：若未使用 nupdown 来指定单电子数量，则对每种原子内每个原子，累加其 mag/magmom，即磁矩模长，赋予 GlobalV::nupdown。❗ 但对于两种方式均赋予，但值不一致的情况未进行处理。
接下来根据在 STRU 中读取的晶胞参数，计算晶胞体积，并计算倒空间矢量（在上篇中已经对 latvec, G, GT, GGT 有所介绍，invGGT 的意义也不言自明）：
-this->omega = std::abs( latvec.Det() ) * this->lat0 * lat0 * lat0 ;
+ this->omega = std::abs( latvec.Det() ) * this->lat0 * lat0 * lat0 ;
this->GT = latvec.Inverse();
this->G = GT.Transpose();
@@ -1442,7 +1436,7 @@ =
static_cast<ModulePW::PW_Basis_Big*>(pw_rho);
对于 ESolver 本身，其指针对象 p_esolver 实际上也有类似操作：
-//Some API to operate E_Solver
+ //Some API to operate E_Solver
void init_esolver(ESolver*& p_esolver)
{
//determine type of esolver based on INPUT information
@@ -1907,7 +1901,7 @@ Introduction to ABACUS: Path to PW calculation - Part 1
下篇：Introduction to ABACUS: Path to PW calculation - Part 3
@@ -1951,7 +1945,7 @@ No results matching "
var gitbook = gitbook || [];
gitbook.push(function() {
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st_bottom2D)","attributes":{},"skip":false,"key":"1.2.9.3"},{"backlink":"develop-path5.html#fig1.2.10.1","level":"1.2.10","list_caption":"Figure: 善用Ctrl+F","alt":"善用Ctrl+F","nro":19,"url":"picture/fig_path5-9.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"善用Ctrl+F","attributes":{},"skip":false,"key":"1.2.10.1"},{"backlink":"develop-path5.html#fig1.2.10.2","level":"1.2.10","list_caption":"Figure: klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","alt":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","nro":20,"url":"picture/fig_path5-10.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","attributes":{},"skip":false,"key":"1.2.10.2"},{"backlink":"develop-path5.html#fig1.2.10.3","level":"1.2.10","list_caption":"Figure: klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","alt":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","nro":21,"url":"picture/fig_path5-11.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","attributes":{},"skip":false,"key":"1.2.10.3"},{"backlink":"develop-path5.html#fig1.2.10.4","level":"1.2.10","list_caption":"Figure: 1-dimensional example","alt":"1-dimensional example","nro":22,"url":"picture/fig_path5-12.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"1-dimensional example","attributes":{},"skip":false,"key":"1.2.10.4"},{"backlink":"develop-path5.html#fig1.2.10.5","level":"1.2.10","list_caption":"Figure: 2-dimensional example","alt":"2-dimensional example","nro":23,"url":"picture/fig_path5-13.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"2-dimensional example","attributes":{},"skip":false,"key":"1.2.10.5"}]},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"develop-path2.md","mtime":"2023-10-04T14:37:12.149Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-10-04T15:29:41.868Z"},"basePath":".","book":{"language":""}});
});
diff --git a/_book/develop-path3.html b/_book/develop-path3.html
index b8de33d9..09176394 100644
--- a/_book/develop-path3.html
+++ b/_book/develop-path3.html
@@ -750,11 +750,11 @@ Driver
-Driver::atomic_world()
-Driver::driver_run()
-多层继承：Init() functions in esolver class
-Trigger: ESolver_FP::Init()
+Driver
+Driver::atomic_world()
+Driver::driver_run()
+多层继承：Init() functions in esolver class
+Trigger: ESolver_FP::Init()
承接上篇中已经导入的结构信息，以及了解到构造函数及其伴随的变量初始化和 ABACUS 里应用到的 C++ 多态编程，接下来即将（逐渐）步入 ABACUS 的核心内容。我们暂时跳过位于 source/driver_run.cpp:driver_run() 的：
// 3. For these two types of calculations
// nothing else need to be initialized
@@ -830,14 +830,14 @@ }
同理，ESolver_KS 的数据成员，也被 ESolver_KS_PW 继承。ESolver_FP::Init() 首先调用 UnitCell::read_pseudo() 函数进行赝势文件读取，而将赝势文件读取任务放在 FP 层级下，也暗示对于 ABACUS 的第一性原理方法实现来讲，都需要使用赝势。
-Pseudopotential import: UnitCell::read_pseudo()
+Pseudopotential import: UnitCell::read_pseudo()
void UnitCell::read_pseudo(std::ofstream &ofs)
{
read_cell_pseudopots(GlobalV::global_pseudo_dir, ofs);
在解读赝势文件读取功能之前，首先需要对赝势文件的结构和信息做一定程度的了解。
-# ONCV pseudopotential file
-## Section 0: Norm-conserving conditions, generation of pseudopotential and header of exact UPF file
+ONCV pseudopotential file
+Section 0: Norm-conserving conditions, generation of pseudopotential and header of exact UPF file
赝势的意义不言自明，其中模守恒赝势需满足如下条件：
- （赝势得到的能级和全电子方法求解的能级一样，这里 ps 代表 pseudopotentials）
@@ -852,7 +852,7 @@ V_l(r)=\frac{1}{\phi^\text{ps}_l(r)}[\epsilon^\text{ps}_l-\frac{\hbar^2}{2m}\frac{l(l+1)}{r^2}+\frac{\hbar^2}{2m}\frac{d^2}{dr^2}]\phi^\text{ps}_l(r)，解得。
- 扣除中 Hartree、xc 部分，得到：。
-更多细节见
+更多细节见：www.tcm.phy.cam.ac.uk
<UPF version="2.0.1">
<PP_INFO>
<!-- omitted information here -->
@@ -865,8 +865,8 @@ <!-- -->
从 UPF 文件（注意 UPF 文件也有不同的版本，目前 ABACUS 都支持，若有不支持的，可以提 Github 的 issues 进行讨论）开始，截止到 <PP_HEADER> 之前，提供了赝势文件的作者信息，引用信息以及生成赝势文件所使用的程序和相应输入文件，并附带输入文件参数中的解释。由于此块内容对实际计算并不起作用，因此暂时略过。
-## Section 1:
-<PP_HEADER
+Section 1:
+ <PP_HEADER
generated="Generated using ONCVPSP code by D. R. Hamann" author="Martin Schlipf and Francois Gygi"
date="150105" comment=""
element="Al"
@@ -890,8 +890,8 @@ number_of_proj
="4"/>
<PP_HEADER> 部分尽管已经位于所谓“not human readable”区域，但也并非如此。这部分“标签”（HTML 语境）/block 实际上包含了众多精简过的信息，如元素名称（element）、赝势类型（pseudo_type，模守恒，norm-conserving，NC），相对论效应（relativistic），是否为超软赝势等等信息。当前 Al 理论上其原子序数 13，因此有 13 个电子，但此处 z_valence 参数为 11，即有两个 1s 电子被赝化，只留下 2s, 2p, 3s, 3p 电子共 2+6+2+1 个。对于某些元素，甚至有大核赝势与小核赝势之分，根据赝化电子数量不同进行区分。显而易见地，赝化电子数量越多，则计算量越小，但计算结果的精确程度可能更低。
-## Section 2:
-<PP_MESH>
+Section 2:
+ <PP_MESH>
<PP_R type="real" size=" 602" columns="8">
0.0000 0.0100 0.0200 0.0300 0.0400 0.0500 0.0600 0.0700
<!-- omitted information here -->
@@ -907,8 +907,8 @@ </PP_MESH>
这部分开始出现了关于实空间格点相关量的定义。在 tag 中不仅指定数据类型为实数，也指定当前数据的长度（size），以及数据存储的列数（columns = 8）。PP_R 为格点坐标，PP_RAB 则为格点间距。
-## Section 3:
-<PP_LOCAL type="real" size=" 602" columns="4">
+Section 3:
+ <PP_LOCAL type="real" size=" 602" columns="4">
-4.5793174225E+01 -4.5788454271E+01 -4.5774276797E+01 -4.5750659428E+01
<!-- omitted information here -->
-3.6912752197E+00 -3.6850921941E+00 -3.6789298138E+00 -3.6727880140E+00
@@ -917,8 +917,8 @@ <PP_LOCAL>
部分开始，正式开始写入赝势的具体数值，建立在 <PP_R> 和 <PP_RAB> 所描述的实空间格点上。。<PP_LOCAL> 正是赝势的局域势部分。
-## Section 4:
-<PP_NONLOCAL>
+Section 4:
+ <PP_NONLOCAL>
<PP_BETA.1
type="real"
size=" 602"
@@ -938,8 +938,8 @@ cutoff_radius_index
=" 246" cutoff_radius=" 2.4500000000E+00" >
<!-- omitted information here -->
</PP_BETA.2>
- <PP_BETA.3 type="real" size=" 602" columns="4" index="3" angular_momentum="1"<strong>
-</strong> cutoff_radius_index=" 246" cutoff_radius=" 2.4500000000E+00" >
+ <PP_BETA.3 type="real" size=" 602" columns="4" index="3" angular_momentum="1"
+ cutoff_radius_index=" 246" cutoff_radius=" 2.4500000000E+00" >
<!-- omitted information here -->
</PP_BETA.3>
<PP_BETA.4 type="real" size=" 602" columns="4" index="4" angular_momentum="1"
@@ -956,7 +956,7 @@ \hat{V}^\text{NL}=\sum_{ij}{|\beta_i\rangle D_{ij}\langle\beta_j|}。其中一般被称为非局域势投影子（projector）。
-## Section 5: and
+Section 5: and
<PP_PSWFC>
</PP_PSWFC>
<PP_RHOATOM type="real" size=" 602" columns="4">
@@ -975,7 +975,7 @@ |\beta\rangle和 pswfc 已经乘径向坐标。
-# UnitCell::read_cell_pseudopots()
+UnitCell::read_cell_pseudopots()
link to Github -> link
void UnitCell::read_cell_pseudopots(const std::string &pp_dir, std::ofstream &log)
{
@@ -1030,7 +1030,7 @@ while (ifs.good())
+ while (ifs.good())
{
ifs >> dummy;
if(dummy=="<PP_HEADER>")
@@ -1044,7 +1044,7 @@ if ( ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_MESH>") )
+ if ( ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_MESH>") )
{
read_pseudo_mesh(ifs);
ModuleBase::GlobalFunc::SCAN_END(ifs, "</PP_MESH>");
@@ -1052,7 +1052,7 @@ if (this->nlcc)
+ if (this->nlcc)
{
ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_NLCC>");
read_pseudo_nlcc(ifs);
@@ -1061,12 +1061,12 @@ ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_LOCAL>");
+ ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_LOCAL>");
read_pseudo_local(ifs);
ModuleBase::GlobalFunc::SCAN_END(ifs, "</PP_LOCAL>");
与 类似的还有 , , , 从 则可以读取旋轨耦合相关信息：
-if (has_so)
+ if (has_so)
{
ModuleBase::GlobalFunc::SCAN_BEGIN (ifs,"<PP_ADDINFO>");
read_pseudo_so (ifs);
@@ -1140,7 +1140,7 @@ if(error==0)
+ if(error==0)
{
if(this->atoms[i].flag_empty_element) upf.set_empty_element();
error_ap = upf.average_p(GlobalV::soc_lambda);
@@ -1148,7 +1148,7 @@ if(GlobalV::MY_RANK==0)
+ if(GlobalV::MY_RANK==0)
{
atoms[i].ncpp.set_pseudo_nc( upf );
....
@@ -1178,7 +1178,7 @@ }
该函数属于类 pseudo_nc，而 pseudo_nc 对象为 atom 的数据成员，atoms 则为 UnitCell 的数据成员。pseudo_nc::set_pseudo_h()，pseudo_nc::set_pseudo_atom 和 pseudo_nc::set_pseudo_vl 的内容在此省略，但其分别为将 Hamilton, 原子性质和 Vlocal 相关数据从 upf 对象拷贝。之后(1)使用 lll 刷新为 upf 对象的 projectors 的角动量，然后计算出磁角动量区分时的 projector 个数。(2)取所有 projector 衰减到 0 时候的最大最普适半径。
-# 赝势信息后处理
+赝势信息后处理
回到 module_cell/unitcell.cpp line 663，接下来为每个原子创建目录，在目录中写 [原子label].NONLOCAL 文件。[label].NONLOCAL 文件中内容包含 <HEADER>, <DIJ> 和 <PP_BETA> 三个 tag。
<HEADER> 中包含内容：
ofs << "<HEADER>" << std::endl;
@@ -1222,21 +1222,61 @@ }
ofs << "</PP_BETA>" << std::endl;
-# 赝势信息分发：UnitCell::bcast_unitcell2(void)
+赝势信息分发：UnitCell::bcast_unitcell2(void)
#ifdef __MPI
+接下来对赝势信息进行MPI进程（processor）间的分发：
+#ifdef __MPI
+ bcast_unitcell2();
+#endif
+
+// module_cell/unitcell.cpp:bcast_unitcell2()
+void UnitCell::bcast_unitcell2(void)
+{
+ for (int i = 0; i < ntype; i++)
+ {
+ atoms[i].bcast_atom2();
+ }
+ return;
+}
+
+// module_cell/atom_spec.cpp:Atom::bcast_atom2()
+void Atom::bcast_atom2()
+{
+ this->ncpp.bcast_atom_pseudo();
+}
+
+// module_cell/atom_pseudo.cpp::Atom_pseudo::bcast_atom_pseudo()
+void Atom_pseudo::bcast_atom_pseudo(void)
+{
+....
+ Parallel_Common::bcast_int( lmax );
+....
+ Parallel_Common::bcast_double( etotps );
+....
+ Parallel_Common::bcast_bool( tvanp );
+....
+ Parallel_Common::bcast_string( psd );
+....
+ // below two 'bcast_double' lines of codes seem to have bugs,
+ // on some computers, the code will stuck here for ever.
+ // mohan note 2021-04-28
+ Parallel_Common::bcast_double( dion.c , nbeta * nbeta);
+ Parallel_Common::bcast_double( betar.c, nr * nc );
+}
+
#endif
-# 赝势信息核对
+赝势信息核对
接下来跨原子种类检验泛函是否一致：
-for(int it=0; it<ntype; it++)
+ for(int it=0; it<ntype; it++)
{
if(atoms[0].ncpp.xc_func !=atoms[it].ncpp.xc_func)
{
-# STRU 结构检查：UnitCell::check_structure()
+STRU 结构检查：UnitCell::check_structure()
检验结构中任意两原子之间距离是否大于其固定倍数（<1）的共价半径和，
-check_structure(GlobalV::MIN_DIST_COEF);
+ check_structure(GlobalV::MIN_DIST_COEF);
-# 计算轨道数：UnitCell::cal_natomwfc()
+计算轨道数：UnitCell::cal_natomwfc()
UnitCell::cal_natomwfc() 函数计算所有种类的原子轨道数量加和，对于非 nspin=4，即非 soc（自旋轨道耦合）情况，角量子数 l 和 s 非耦合，l 单独可以作为好的量子数来区分量子态，因此对于每个赝势中定义的 wfc，若其对应 occupation 大于等于 0（即有效 wfc），则对应于其角量子数 l，轨道数量增加 2l+1，即计数其磁量子数 m，也相当于对 alpha 和 beta spin 的单独计数。对于 nspin=4 的情况，若考虑 soc，则轨道数对 j=l+s 的情况，当前原子种类当前角量子数对应轨道数量记为 2l+1+1，否则为 2l+1。对于非 soc 但 nspin=4，当前原子种类轨道当前角量子数对应轨道数量记(2l+1)*2：
void UnitCell::cal_natomwfc(std::ofstream &log)
{
@@ -1291,9 +1331,9 @@ 计算跨原子种类最大角量子数 UnitCell::lmax 和某 l 对应最大 zeta 数 UnitCell::nmax，以及跨原子种类的类内 zeta 数总和最大值 UnitCell::nmax_total
寻找赝势中最大角量子数 UnitCell::lmax_ppwf。
-# 价电子数核对
+价电子数核对
核对赝势中定义的价电子数与 ABACUS 预置库中原子的最小价电子数
-# 获取最大格点数量：UnitCell::cal_meshx()
+获取最大格点数量：UnitCell::cal_meshx()
计算跨原子种类的最大格点数量，存储在 UnitCell::meshx 中，目前 ABACUS 代码中变量命名后缀 x 可能代表 max，正如之前看到 npwx 等。
至此，我们离开函数 UnitCell::read_pseudo()，回到 ModuleESolver::ESolver_FP::Init() 函数。
@@ -1304,7 +1344,7 @@ Introduction to ABACUS: Path to PW calculation - Part 2
下篇：Introduction to ABACUS: Path to PW calculation - Part 4
@@ -1348,7 +1388,7 @@ No results matching "
var gitbook = gitbook || [];
gitbook.push(function() {
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example","attributes":{},"skip":false,"key":"1.2.10.5"}]},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"develop-path3.md","mtime":"2023-10-04T15:11:45.401Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-10-04T15:29:41.868Z"},"basePath":".","book":{"language":""}});
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diff --git a/_book/develop-path4.html b/_book/develop-path4.html
index 1840948c..2b9cddf9 100644
--- a/_book/develop-path4.html
+++ b/_book/develop-path4.html
@@ -750,14 +750,14 @@ Driver
-Driver::atomic_world()
-Driver::driver_run()
-多层继承：Init() functions in esolver class
-Trigger: ESolver_FP::Init()
-平面波格点初始化：PW_Basis:: initgrids()
+Driver
+Driver::atomic_world()
+Driver::driver_run()
+多层继承：Init() functions in esolver class
+Trigger: ESolver_FP::Init()
+平面波格点初始化：PW_Basis:: initgrids()
完成了 INPUT 和 STRU，以及赝势文件的读取环节，接下来我们来到平面波的初始化设置相关部分。
-void ESolver_FP::Init(Input& inp, UnitCell& cell)
+ void ESolver_FP::Init(Input& inp, UnitCell& cell)
{
....
if (inp.nx * inp.ny * inp.nz == 0)
@@ -782,7 +782,7 @@ virtual void initgrids(const double lat0_in,const ModuleBase::Matrix3 latvec_in,
+ virtual void initgrids(const double lat0_in,const ModuleBase::Matrix3 latvec_in,
const double gridecut)
{
// generation of nx, ny and nz are omitted here
@@ -868,7 +868,7 @@ }
❗ 注意：这里还完成了倒空间格点数量 fftnx, fftny 和 fftnz 的赋值。因为 FFT 变换前后的格点数量一般相同，因此 fftnx = nx，fftny = ny，...。
-
+图 1. 然后对平面波在 MPI 进程间进行分发：
//module_esolver/esolver_fp.cpp
void ESolver_FP::Init(Input& inp, UnitCell& cell)
@@ -889,9 +889,9 @@ ::
timer::tick(this->classname, "setuptransform");
}
-PW_Basis::setuptransform()（link）
-# 并行机制简述
-## 并行池
+PW_Basis::setuptransform()（link）
+并行机制简述
+并行池
到这里，我们不得不开始对平面波的 MPI 并行机制有一个大致的认识。在 ABACUS 中，CPU（=processor）首先根据不同的布里渊区 k 点分组被划分成不同的并行池（parallelizaiton pool），每个 pool 都包含几个 k 点，在每个 pool 里面会有完整的对该 k 点求解 Kohn-Sham 方程的过程。因此，在每个 pool 中采用一定数量的 CPU 进程来完成计算。在 INPUT 文件中，KPAR 参数决定了并行池的数量（即 pool 的个数）。换句话说，ABACUS 的 k 点并行机制为，将 k 点（设其数量为 nkpt）分配在 KPAR 个 pool 中，若一共有 nproc 个 processor，则：
- 每个 pool 有
nproc/KPAR 个 processor
@@ -899,7 +899,7 @@ ## MPI 进程编号：rank
+MPI 进程编号：rank
rank 是一个在 MPI 并行里常被用到的变量。在拥有不止一个 processor 的时候，每个 processor 都具有唯一的编号，称为 rank。如果在每个 processor 都有 rank 的基础上还定义了 pool，以及在每个 pool 中的 processor 数量，则 processor 除了有跨 pool 的全局 rank，也可以有 pool 之内的局部 rank，这部分内容见 module_base/global_variable.cpp:
int NPROC = 1;
int KPAR = 1;
@@ -926,7 +926,7 @@ }
}
-## 并行策略
+并行策略
于是问题便到来：在并行条件下，代码究竟是如何执行的？
- 对于多核 CPU，是否运行在其上的所有程序都进行了并行化？
@@ -950,9 +950,9 @@ ## OpenMP-MPI 混合编程
+OpenMP-MPI 混合编程
通常来讲，尽管 OpenMP 提供了线程并行，但由于共享内存可能并不存在于 processors 之间，或 computer, nodes 之间，且没有适合的内存共享系统（multi-socket server），此时如果以 OpenMP 放心运行，则可能得出错误结果或直接报错——因为内存无法访问。对于这种情况，需要使用 MPI（Message passing interface）来维持无内存共享处理单元之间的信息交换，以及信息分发和分布计算，而在处理单元内部，即可以共享内存的域内，则可以通过 OpenMP 技术来进行线程级并行。
-# 实空间格点分发
+实空间格点分发
在简单介绍完并行机制后，我们知道，对于未显式以并行方式实现的函数，其运行将在每一个 processor。在接下来的平面波分发过程中，请始终牢记这一理念，尤其在 processor-local 变量和 processor-global 变量的传值过程中。
稍加回溯：
void ESolver_FP::Init(Input& inp, UnitCell& cell)
@@ -968,7 +968,7 @@ ## 实空间：PW_Basis::distribute_r()
+实空间：PW_Basis::distribute_r()
❗Attention
注意，此时实际调用的也是 PW_Basis_Big 而非 PW_Basis 的 distribute_r() 函数。
@@ -1011,8 +1011,8 @@ {
....
该判断不会 always true。因此 PW_Basis::distribute_r() 将 3D 实空间格点，按照 z 方向进行分发，分给了不同的 processors，并赋值 this->npz，this->nplane, this->startz_current 和 this->nrxx，意义分别为当前 processor 的 z 方向格点数量、xy 平面数量、z 格点的起始索引以及当前 processor 所分得实空间格点总数（分配后 z 方向格点 ×xy 平面格点）。
-
-## 倒空间：PW_Basis::distribute_g()
+图 2. PW_Basis::distribute_r()：设一个pool中有5个processors 倒空间：PW_Basis::distribute_g()
倒空间格点的分发采用了和实空间不同的方式，这主要是因为倒空间“球”的存在（ecutwfc 和 ecutrho），使得非空间中所有点都需要考虑在内，而实空间则并非如此。更一般而言，有限的实空间带来无限的倒空间（即实空间 delta 函数需要无限数量的平面波展开）延展，而有限的倒空间（倒空间 delta 点）带来无限的实空间延展（如一个平面波）。
🔧重构信息
@@ -1066,7 +1066,7 @@
delete
[] st_bottom2D; delete[] st_length2D;
}
-### 分发最小单元：“棍子” - 准备工作
+分发最小单元：“棍子” - 准备工作
穿过布里渊区的整数点（2pi/a 的整数倍）都代表一个三个 index 的平面波，而一系列的点在截断半径以内沿着某个方向就组成了所谓的“stick”（代表平面波集合的“棍子”，一个“棍子”包含了多个平面波，简称就叫“棍子”）。
PW_Basis::count_pw_st() 函数（Link）计算了每个(x,y)对应的“棍子”的底部和“长度”，即对倒空间只分辨(x,y)，则会得到沿 z 方向的点的集合，被称为“棍子”。而“棍子”区域内部每一个点都代表一个平面波。“棍子”的底部对应于最小的 iz 值，“根子”的长度则为当前(x,y)所包含的平面波数量：
for (int ix = ix_start; ix <= ix_end; ++ix)
@@ -1098,7 +1098,7 @@ }
}
-
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diff --git a/_book/develop-path1.html b/_book/develop-path1.html
index 1de92b86..d41c1be3 100644
--- a/_book/develop-path1.html
+++ b/_book/develop-path1.html
@@ -1112,8 +1112,8 @@ <
Input_Conv::Convert()
这个函数实现了从 Input 类对象的数据成员到 GlobalV 和 GlobalC 等全局变量集合的转换。相当于从 Input 到 GlobalV 和 GlobalC，以及其他直接的类的参数上载：
-其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
+其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
void Input_Conv::Convert(void)
{
....
@@ -1308,7 +1308,7 @@
不要忘记我们已经完成 Driver::reading() 函数内容，到达 Driver::atomic_world()。这一点从本文档设置的分级目录中也可以看得到。
-cppvoid Driver::init()
+void Driver::init()
{
this->reading();
this->atomic_world(); // <- here!
@@ -1518,7 +1518,7 @@ 从 SIAB 到 ABACUS（一）：准备工作（施工中 🚧）
下篇：Introduction to ABACUS: Path to PW calculation - Part 2
@@ -1562,7 +1562,7 @@ No results matching "
var gitbook = gitbook || [];
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index 191dfe74..d829579b 100644
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@@ -1028,7 +1028,7 @@ // a(i) is lattice vector
}
-我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
+我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
UnitCell::read_atom_positions()
🔧重构思考
@@ -1042,7 +1042,7 @@
::
GlobalFunc::READ_VALUE( ifpos, Coordinate);
STRU 第二行指定坐标类型，被读取为 UnitCell::Coordinate。UnitCell::Coordinate 在 STRU 里有不同选项，⚙ 决定原子的具体位置和单位：
-if(Coordinate != "Cartesian"
+ if(Coordinate != "Cartesian"
&& Coordinate != "Direct"
&& Coordinate != "Cartesian_angstrom"
&& Coordinate != "Cartesian_au"
@@ -1092,7 +1092,7 @@ int na = 0;
+ int na = 0;
this->nat = 0;
assert(ntype>0);
for (int it = 0;it < ntype; it++)
@@ -1105,7 +1105,7 @@ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
bool sequence_match = false;
for(int it2=0; it2<ntype; it2++)
{
@@ -1121,7 +1121,7 @@ }
读取当前原子类型的 starting_magnetization、原子总数 na
-ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
...
ModuleBase::GlobalFunc::READ_VALUE(ifpos, na);
this->atoms[it].na = na;
@@ -1149,17 +1149,17 @@ [
it].m_loc_ = new ModuleBase::Vector3<double>[na];
⚙ 然后在 ATOMIC_POSITIONS 中读取：
-atoms[it].mass = this->atom_mass[it];
+ atoms[it].mass = this->atom_mass[it];
❗ 此处的 atoms[it].mass 与 this->atom_mass[it] 的用法与 atomis[it].label 与 this->atom_label[it] 不同：传值 vs 核对。
接下来读取类中每个原子的速度信息，在做分子动力学模拟的时候可能需要用到：
-for (int ia = 0;ia < na; ia++)
+ for (int ia = 0;ia < na; ia++)
{
ifpos >> v.x >> v.y >> v.z;
然而，当前 STRU 文件在 ATOMIC_POSITIONS 的设计比较复杂，其可以包括任何一组 atom-specific 数据，且数量和顺序均不受限制，这导致判断条件变得复杂，详见 module_cell/read_atoms.cpp:line 536 - 567（link）。
atoms[it].mag 的赋值并非直接读取：
-else if ( tmpid == "mag" || tmpid == "magmom")
+ else if ( tmpid == "mag" || tmpid == "magmom")
{
set_element_mag_zero = true;
double tmpamg=0; ifpos >> tmpamg;
@@ -1185,7 +1185,7 @@ }
⚙ 若 mag/magmom 后有一个值，则读取其值赋给 atoms[it]::mag[ia]，将 input_vec_mag 置为 false，若有三个值，则三个值依次被传入 atoms[it].m_loc_[ia].x, atoms[it].m_loc_[ia].y 和 atoms[it].m_loc_[ia].z，并将 input_vec_mag 置为 true，之后其向量模长为 atoms[it]::mag[ia]，然后在使用 angle1, angle2 来重新生成 mag。
-if(GlobalV::NSPIN==4)
+ if(GlobalV::NSPIN==4)
{
if(GlobalV::NONCOLIN)
{
@@ -1227,7 +1227,7 @@ pw.x input description
ABACUS 对 nspin=4 情况的参数处理：
//module_io/input_conv.cpp line 376
if (INPUT.noncolin || INPUT.lspinorb)
@@ -1312,7 +1312,7 @@
UnitCell::setup_cell(): the rest, and an example of backtracking unclear variable
离开 STRU 文件的解析部分，接下来计算了初始磁化强度：
-//after read STRU, calculate initial total magnetization when NSPIN=2
+ //after read STRU, calculate initial total magnetization when NSPIN=2
if(GlobalV::NSPIN == 2 && !GlobalV::TWO_EFERMI)
{
for(int it = 0;it<this->ntype; it++)
@@ -1326,31 +1326,25 @@ if (std::abs(INPUT.nupdown) > 1e-6)
- {
- GlobalV::TWO_EFERMI = true;
- GlobalV::nupdown = INPUT.nupdown;
- }
-
-因此 GlobalV::TWO_EFERMI 变量实际依赖于 INPUT.nupdown。
-
-- 接下来在
module_io/input.cpp 中寻找含 INPUT.nupdown 的 if(strcmp(...)) 单元，查看在 INPUT 文件中是何参数赋予其具体值：
-
-else if (strcmp("nupdown", word) == 0)
+在 module_io/input_conv.cpp 中寻找该变量，是何变量赋其值，发现： if (std::abs(INPUT.nupdown) > 1e-6)
{
- read_value(ifs, nupdown);
- }
+ GlobalV::TWO_EFERMI = true;
+ GlobalV::nupdown = INPUT.nupdown;
+ }
-即 INPUT.nupdown 在 INPUT 中也为 nupdown。接下来打开 Full keyword list 寻找其解释。
-
+ 因此 GlobalV::TWO_EFERMI 变量实际依赖于 INPUT.nupdown。
+接下来在 module_io/input.cpp 中寻找含 INPUT.nupdown 的 if(strcmp(...)) 单元，查看在 INPUT 文件中是何参数赋予其具体值： else if (strcmp("nupdown", word) == 0)
+ {
+ read_value(ifs, nupdown);
+ }
+
+即 INPUT.nupdown 在 INPUT 中也为 nupdown。接下来打开 Full keyword list 寻找其解释。
得到结果，即 nupdown 为 spin up 和 spin down 电子数量差值：
因此该部分逻辑为：若未使用 nupdown 来指定单电子数量，则对每种原子内每个原子，累加其 mag/magmom，即磁矩模长，赋予 GlobalV::nupdown。❗ 但对于两种方式均赋予，但值不一致的情况未进行处理。
接下来根据在 STRU 中读取的晶胞参数，计算晶胞体积，并计算倒空间矢量（在上篇中已经对 latvec, G, GT, GGT 有所介绍，invGGT 的意义也不言自明）：
-this->omega = std::abs( latvec.Det() ) * this->lat0 * lat0 * lat0 ;
+ this->omega = std::abs( latvec.Det() ) * this->lat0 * lat0 * lat0 ;
this->GT = latvec.Inverse();
this->G = GT.Transpose();
@@ -1442,7 +1436,7 @@ =
static_cast<ModulePW::PW_Basis_Big*>(pw_rho);
对于 ESolver 本身，其指针对象 p_esolver 实际上也有类似操作：
-//Some API to operate E_Solver
+ //Some API to operate E_Solver
void init_esolver(ESolver*& p_esolver)
{
//determine type of esolver based on INPUT information
@@ -1907,7 +1901,7 @@ Introduction to ABACUS: Path to PW calculation - Part 1
下篇：Introduction to ABACUS: Path to PW calculation - Part 3
@@ -1951,7 +1945,7 @@ No results matching "
var gitbook = gitbook || [];
gitbook.push(function() {
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st_bottom2D)","attributes":{},"skip":false,"key":"1.2.9.3"},{"backlink":"develop-path5.html#fig1.2.10.1","level":"1.2.10","list_caption":"Figure: 善用Ctrl+F","alt":"善用Ctrl+F","nro":19,"url":"picture/fig_path5-9.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"善用Ctrl+F","attributes":{},"skip":false,"key":"1.2.10.1"},{"backlink":"develop-path5.html#fig1.2.10.2","level":"1.2.10","list_caption":"Figure: klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","alt":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","nro":20,"url":"picture/fig_path5-10.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","attributes":{},"skip":false,"key":"1.2.10.2"},{"backlink":"develop-path5.html#fig1.2.10.3","level":"1.2.10","list_caption":"Figure: klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","alt":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","nro":21,"url":"picture/fig_path5-11.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","attributes":{},"skip":false,"key":"1.2.10.3"},{"backlink":"develop-path5.html#fig1.2.10.4","level":"1.2.10","list_caption":"Figure: 1-dimensional example","alt":"1-dimensional example","nro":22,"url":"picture/fig_path5-12.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"1-dimensional example","attributes":{},"skip":false,"key":"1.2.10.4"},{"backlink":"develop-path5.html#fig1.2.10.5","level":"1.2.10","list_caption":"Figure: 2-dimensional example","alt":"2-dimensional example","nro":23,"url":"picture/fig_path5-13.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"2-dimensional example","attributes":{},"skip":false,"key":"1.2.10.5"}]},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"develop-path2.md","mtime":"2023-10-04T14:37:12.149Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-10-04T15:29:41.868Z"},"basePath":".","book":{"language":""}});
});
diff --git a/_book/develop-path3.html b/_book/develop-path3.html
index b8de33d9..09176394 100644
--- a/_book/develop-path3.html
+++ b/_book/develop-path3.html
@@ -750,11 +750,11 @@ Driver
-Driver::atomic_world()
-Driver::driver_run()
-多层继承：Init() functions in esolver class
-Trigger: ESolver_FP::Init()
+Driver
+Driver::atomic_world()
+Driver::driver_run()
+多层继承：Init() functions in esolver class
+Trigger: ESolver_FP::Init()
承接上篇中已经导入的结构信息，以及了解到构造函数及其伴随的变量初始化和 ABACUS 里应用到的 C++ 多态编程，接下来即将（逐渐）步入 ABACUS 的核心内容。我们暂时跳过位于 source/driver_run.cpp:driver_run() 的：
// 3. For these two types of calculations
// nothing else need to be initialized
@@ -830,14 +830,14 @@ }
同理，ESolver_KS 的数据成员，也被 ESolver_KS_PW 继承。ESolver_FP::Init() 首先调用 UnitCell::read_pseudo() 函数进行赝势文件读取，而将赝势文件读取任务放在 FP 层级下，也暗示对于 ABACUS 的第一性原理方法实现来讲，都需要使用赝势。
-Pseudopotential import: UnitCell::read_pseudo()
+Pseudopotential import: UnitCell::read_pseudo()
void UnitCell::read_pseudo(std::ofstream &ofs)
{
read_cell_pseudopots(GlobalV::global_pseudo_dir, ofs);
在解读赝势文件读取功能之前，首先需要对赝势文件的结构和信息做一定程度的了解。
-# ONCV pseudopotential file
-## Section 0: Norm-conserving conditions, generation of pseudopotential and header of exact UPF file
+ONCV pseudopotential file
+Section 0: Norm-conserving conditions, generation of pseudopotential and header of exact UPF file
赝势的意义不言自明，其中模守恒赝势需满足如下条件：
- （赝势得到的能级和全电子方法求解的能级一样，这里 ps 代表 pseudopotentials）
@@ -852,7 +852,7 @@ V_l(r)=\frac{1}{\phi^\text{ps}_l(r)}[\epsilon^\text{ps}_l-\frac{\hbar^2}{2m}\frac{l(l+1)}{r^2}+\frac{\hbar^2}{2m}\frac{d^2}{dr^2}]\phi^\text{ps}_l(r)，解得。
- 扣除中 Hartree、xc 部分，得到：。
-更多细节见
+更多细节见：www.tcm.phy.cam.ac.uk
<UPF version="2.0.1">
<PP_INFO>
<!-- omitted information here -->
@@ -865,8 +865,8 @@ <!-- -->
从 UPF 文件（注意 UPF 文件也有不同的版本，目前 ABACUS 都支持，若有不支持的，可以提 Github 的 issues 进行讨论）开始，截止到 <PP_HEADER> 之前，提供了赝势文件的作者信息，引用信息以及生成赝势文件所使用的程序和相应输入文件，并附带输入文件参数中的解释。由于此块内容对实际计算并不起作用，因此暂时略过。
-## Section 1:
-<PP_HEADER
+Section 1:
+ <PP_HEADER
generated="Generated using ONCVPSP code by D. R. Hamann" author="Martin Schlipf and Francois Gygi"
date="150105" comment=""
element="Al"
@@ -890,8 +890,8 @@ number_of_proj
="4"/>
<PP_HEADER> 部分尽管已经位于所谓“not human readable”区域，但也并非如此。这部分“标签”（HTML 语境）/block 实际上包含了众多精简过的信息，如元素名称（element）、赝势类型（pseudo_type，模守恒，norm-conserving，NC），相对论效应（relativistic），是否为超软赝势等等信息。当前 Al 理论上其原子序数 13，因此有 13 个电子，但此处 z_valence 参数为 11，即有两个 1s 电子被赝化，只留下 2s, 2p, 3s, 3p 电子共 2+6+2+1 个。对于某些元素，甚至有大核赝势与小核赝势之分，根据赝化电子数量不同进行区分。显而易见地，赝化电子数量越多，则计算量越小，但计算结果的精确程度可能更低。
-## Section 2:
-<PP_MESH>
+Section 2:
+ <PP_MESH>
<PP_R type="real" size=" 602" columns="8">
0.0000 0.0100 0.0200 0.0300 0.0400 0.0500 0.0600 0.0700
<!-- omitted information here -->
@@ -907,8 +907,8 @@ </PP_MESH>
这部分开始出现了关于实空间格点相关量的定义。在 tag 中不仅指定数据类型为实数，也指定当前数据的长度（size），以及数据存储的列数（columns = 8）。PP_R 为格点坐标，PP_RAB 则为格点间距。
-## Section 3:
-<PP_LOCAL type="real" size=" 602" columns="4">
+Section 3:
+ <PP_LOCAL type="real" size=" 602" columns="4">
-4.5793174225E+01 -4.5788454271E+01 -4.5774276797E+01 -4.5750659428E+01
<!-- omitted information here -->
-3.6912752197E+00 -3.6850921941E+00 -3.6789298138E+00 -3.6727880140E+00
@@ -917,8 +917,8 @@ <PP_LOCAL>
部分开始，正式开始写入赝势的具体数值，建立在 <PP_R> 和 <PP_RAB> 所描述的实空间格点上。。<PP_LOCAL> 正是赝势的局域势部分。
-## Section 4:
-<PP_NONLOCAL>
+Section 4:
+ <PP_NONLOCAL>
<PP_BETA.1
type="real"
size=" 602"
@@ -938,8 +938,8 @@ cutoff_radius_index
=" 246" cutoff_radius=" 2.4500000000E+00" >
<!-- omitted information here -->
</PP_BETA.2>
- <PP_BETA.3 type="real" size=" 602" columns="4" index="3" angular_momentum="1"<strong>
-</strong> cutoff_radius_index=" 246" cutoff_radius=" 2.4500000000E+00" >
+ <PP_BETA.3 type="real" size=" 602" columns="4" index="3" angular_momentum="1"
+ cutoff_radius_index=" 246" cutoff_radius=" 2.4500000000E+00" >
<!-- omitted information here -->
</PP_BETA.3>
<PP_BETA.4 type="real" size=" 602" columns="4" index="4" angular_momentum="1"
@@ -956,7 +956,7 @@ \hat{V}^\text{NL}=\sum_{ij}{|\beta_i\rangle D_{ij}\langle\beta_j|}。其中一般被称为非局域势投影子（projector）。
-## Section 5: and
+Section 5: and
<PP_PSWFC>
</PP_PSWFC>
<PP_RHOATOM type="real" size=" 602" columns="4">
@@ -975,7 +975,7 @@ |\beta\rangle和 pswfc 已经乘径向坐标。
-# UnitCell::read_cell_pseudopots()
+UnitCell::read_cell_pseudopots()
link to Github -> link
void UnitCell::read_cell_pseudopots(const std::string &pp_dir, std::ofstream &log)
{
@@ -1030,7 +1030,7 @@ while (ifs.good())
+ while (ifs.good())
{
ifs >> dummy;
if(dummy=="<PP_HEADER>")
@@ -1044,7 +1044,7 @@ if ( ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_MESH>") )
+ if ( ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_MESH>") )
{
read_pseudo_mesh(ifs);
ModuleBase::GlobalFunc::SCAN_END(ifs, "</PP_MESH>");
@@ -1052,7 +1052,7 @@ if (this->nlcc)
+ if (this->nlcc)
{
ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_NLCC>");
read_pseudo_nlcc(ifs);
@@ -1061,12 +1061,12 @@ ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_LOCAL>");
+ ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_LOCAL>");
read_pseudo_local(ifs);
ModuleBase::GlobalFunc::SCAN_END(ifs, "</PP_LOCAL>");
与 类似的还有 , , , 从 则可以读取旋轨耦合相关信息：
-if (has_so)
+ if (has_so)
{
ModuleBase::GlobalFunc::SCAN_BEGIN (ifs,"<PP_ADDINFO>");
read_pseudo_so (ifs);
@@ -1140,7 +1140,7 @@ if(error==0)
+ if(error==0)
{
if(this->atoms[i].flag_empty_element) upf.set_empty_element();
error_ap = upf.average_p(GlobalV::soc_lambda);
@@ -1148,7 +1148,7 @@ if(GlobalV::MY_RANK==0)
+ if(GlobalV::MY_RANK==0)
{
atoms[i].ncpp.set_pseudo_nc( upf );
....
@@ -1178,7 +1178,7 @@ }
该函数属于类 pseudo_nc，而 pseudo_nc 对象为 atom 的数据成员，atoms 则为 UnitCell 的数据成员。pseudo_nc::set_pseudo_h()，pseudo_nc::set_pseudo_atom 和 pseudo_nc::set_pseudo_vl 的内容在此省略，但其分别为将 Hamilton, 原子性质和 Vlocal 相关数据从 upf 对象拷贝。之后(1)使用 lll 刷新为 upf 对象的 projectors 的角动量，然后计算出磁角动量区分时的 projector 个数。(2)取所有 projector 衰减到 0 时候的最大最普适半径。
-# 赝势信息后处理
+赝势信息后处理
回到 module_cell/unitcell.cpp line 663，接下来为每个原子创建目录，在目录中写 [原子label].NONLOCAL 文件。[label].NONLOCAL 文件中内容包含 <HEADER>, <DIJ> 和 <PP_BETA> 三个 tag。
<HEADER> 中包含内容：
ofs << "<HEADER>" << std::endl;
@@ -1222,21 +1222,61 @@ }
ofs << "</PP_BETA>" << std::endl;
-# 赝势信息分发：UnitCell::bcast_unitcell2(void)
+赝势信息分发：UnitCell::bcast_unitcell2(void)
#ifdef __MPI
+接下来对赝势信息进行MPI进程（processor）间的分发：
+#ifdef __MPI
+ bcast_unitcell2();
+#endif
+
+// module_cell/unitcell.cpp:bcast_unitcell2()
+void UnitCell::bcast_unitcell2(void)
+{
+ for (int i = 0; i < ntype; i++)
+ {
+ atoms[i].bcast_atom2();
+ }
+ return;
+}
+
+// module_cell/atom_spec.cpp:Atom::bcast_atom2()
+void Atom::bcast_atom2()
+{
+ this->ncpp.bcast_atom_pseudo();
+}
+
+// module_cell/atom_pseudo.cpp::Atom_pseudo::bcast_atom_pseudo()
+void Atom_pseudo::bcast_atom_pseudo(void)
+{
+....
+ Parallel_Common::bcast_int( lmax );
+....
+ Parallel_Common::bcast_double( etotps );
+....
+ Parallel_Common::bcast_bool( tvanp );
+....
+ Parallel_Common::bcast_string( psd );
+....
+ // below two 'bcast_double' lines of codes seem to have bugs,
+ // on some computers, the code will stuck here for ever.
+ // mohan note 2021-04-28
+ Parallel_Common::bcast_double( dion.c , nbeta * nbeta);
+ Parallel_Common::bcast_double( betar.c, nr * nc );
+}
+
#endif
-# 赝势信息核对
+赝势信息核对
接下来跨原子种类检验泛函是否一致：
-for(int it=0; it<ntype; it++)
+ for(int it=0; it<ntype; it++)
{
if(atoms[0].ncpp.xc_func !=atoms[it].ncpp.xc_func)
{
-# STRU 结构检查：UnitCell::check_structure()
+STRU 结构检查：UnitCell::check_structure()
检验结构中任意两原子之间距离是否大于其固定倍数（<1）的共价半径和，
-check_structure(GlobalV::MIN_DIST_COEF);
+ check_structure(GlobalV::MIN_DIST_COEF);
-# 计算轨道数：UnitCell::cal_natomwfc()
+计算轨道数：UnitCell::cal_natomwfc()
UnitCell::cal_natomwfc() 函数计算所有种类的原子轨道数量加和，对于非 nspin=4，即非 soc（自旋轨道耦合）情况，角量子数 l 和 s 非耦合，l 单独可以作为好的量子数来区分量子态，因此对于每个赝势中定义的 wfc，若其对应 occupation 大于等于 0（即有效 wfc），则对应于其角量子数 l，轨道数量增加 2l+1，即计数其磁量子数 m，也相当于对 alpha 和 beta spin 的单独计数。对于 nspin=4 的情况，若考虑 soc，则轨道数对 j=l+s 的情况，当前原子种类当前角量子数对应轨道数量记为 2l+1+1，否则为 2l+1。对于非 soc 但 nspin=4，当前原子种类轨道当前角量子数对应轨道数量记(2l+1)*2：
void UnitCell::cal_natomwfc(std::ofstream &log)
{
@@ -1291,9 +1331,9 @@ 计算跨原子种类最大角量子数 UnitCell::lmax 和某 l 对应最大 zeta 数 UnitCell::nmax，以及跨原子种类的类内 zeta 数总和最大值 UnitCell::nmax_total
寻找赝势中最大角量子数 UnitCell::lmax_ppwf。
-# 价电子数核对
+价电子数核对
核对赝势中定义的价电子数与 ABACUS 预置库中原子的最小价电子数
-# 获取最大格点数量：UnitCell::cal_meshx()
+获取最大格点数量：UnitCell::cal_meshx()
计算跨原子种类的最大格点数量，存储在 UnitCell::meshx 中，目前 ABACUS 代码中变量命名后缀 x 可能代表 max，正如之前看到 npwx 等。
至此，我们离开函数 UnitCell::read_pseudo()，回到 ModuleESolver::ESolver_FP::Init() 函数。
@@ -1304,7 +1344,7 @@ Introduction to ABACUS: Path to PW calculation - Part 2
下篇：Introduction to ABACUS: Path to PW calculation - Part 4
@@ -1348,7 +1388,7 @@ No results matching "
var gitbook = gitbook || [];
gitbook.push(function() {
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1)","alt":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","nro":21,"url":"picture/fig_path5-11.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","attributes":{},"skip":false,"key":"1.2.10.3"},{"backlink":"develop-path5.html#fig1.2.10.4","level":"1.2.10","list_caption":"Figure: 1-dimensional example","alt":"1-dimensional example","nro":22,"url":"picture/fig_path5-12.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"1-dimensional example","attributes":{},"skip":false,"key":"1.2.10.4"},{"backlink":"develop-path5.html#fig1.2.10.5","level":"1.2.10","list_caption":"Figure: 2-dimensional example","alt":"2-dimensional example","nro":23,"url":"picture/fig_path5-13.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"2-dimensional 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diff --git a/_book/develop-path4.html b/_book/develop-path4.html
index 1840948c..2b9cddf9 100644
--- a/_book/develop-path4.html
+++ b/_book/develop-path4.html
@@ -750,14 +750,14 @@ Driver
-Driver::atomic_world()
-Driver::driver_run()
-多层继承：Init() functions in esolver class
-Trigger: ESolver_FP::Init()
-平面波格点初始化：PW_Basis:: initgrids()
+Driver
+Driver::atomic_world()
+Driver::driver_run()
+多层继承：Init() functions in esolver class
+Trigger: ESolver_FP::Init()
+平面波格点初始化：PW_Basis:: initgrids()
完成了 INPUT 和 STRU，以及赝势文件的读取环节，接下来我们来到平面波的初始化设置相关部分。
-void ESolver_FP::Init(Input& inp, UnitCell& cell)
+ void ESolver_FP::Init(Input& inp, UnitCell& cell)
{
....
if (inp.nx * inp.ny * inp.nz == 0)
@@ -782,7 +782,7 @@ virtual void initgrids(const double lat0_in,const ModuleBase::Matrix3 latvec_in,
+ virtual void initgrids(const double lat0_in,const ModuleBase::Matrix3 latvec_in,
const double gridecut)
{
// generation of nx, ny and nz are omitted here
@@ -868,7 +868,7 @@ }
❗ 注意：这里还完成了倒空间格点数量 fftnx, fftny 和 fftnz 的赋值。因为 FFT 变换前后的格点数量一般相同，因此 fftnx = nx，fftny = ny，...。
-
+图 1. 然后对平面波在 MPI 进程间进行分发：
//module_esolver/esolver_fp.cpp
void ESolver_FP::Init(Input& inp, UnitCell& cell)
@@ -889,9 +889,9 @@ ::
timer::tick(this->classname, "setuptransform");
}
-PW_Basis::setuptransform()（link）
-# 并行机制简述
-## 并行池
+PW_Basis::setuptransform()（link）
+并行机制简述
+并行池
到这里，我们不得不开始对平面波的 MPI 并行机制有一个大致的认识。在 ABACUS 中，CPU（=processor）首先根据不同的布里渊区 k 点分组被划分成不同的并行池（parallelizaiton pool），每个 pool 都包含几个 k 点，在每个 pool 里面会有完整的对该 k 点求解 Kohn-Sham 方程的过程。因此，在每个 pool 中采用一定数量的 CPU 进程来完成计算。在 INPUT 文件中，KPAR 参数决定了并行池的数量（即 pool 的个数）。换句话说，ABACUS 的 k 点并行机制为，将 k 点（设其数量为 nkpt）分配在 KPAR 个 pool 中，若一共有 nproc 个 processor，则：
- 每个 pool 有
nproc/KPAR 个 processor
@@ -899,7 +899,7 @@ ## MPI 进程编号：rank
+MPI 进程编号：rank
rank 是一个在 MPI 并行里常被用到的变量。在拥有不止一个 processor 的时候，每个 processor 都具有唯一的编号，称为 rank。如果在每个 processor 都有 rank 的基础上还定义了 pool，以及在每个 pool 中的 processor 数量，则 processor 除了有跨 pool 的全局 rank，也可以有 pool 之内的局部 rank，这部分内容见 module_base/global_variable.cpp:
int NPROC = 1;
int KPAR = 1;
@@ -926,7 +926,7 @@ }
}
-## 并行策略
+并行策略
于是问题便到来：在并行条件下，代码究竟是如何执行的？
- 对于多核 CPU，是否运行在其上的所有程序都进行了并行化？
@@ -950,9 +950,9 @@ ## OpenMP-MPI 混合编程
+OpenMP-MPI 混合编程
通常来讲，尽管 OpenMP 提供了线程并行，但由于共享内存可能并不存在于 processors 之间，或 computer, nodes 之间，且没有适合的内存共享系统（multi-socket server），此时如果以 OpenMP 放心运行，则可能得出错误结果或直接报错——因为内存无法访问。对于这种情况，需要使用 MPI（Message passing interface）来维持无内存共享处理单元之间的信息交换，以及信息分发和分布计算，而在处理单元内部，即可以共享内存的域内，则可以通过 OpenMP 技术来进行线程级并行。
-# 实空间格点分发
+实空间格点分发
在简单介绍完并行机制后，我们知道，对于未显式以并行方式实现的函数，其运行将在每一个 processor。在接下来的平面波分发过程中，请始终牢记这一理念，尤其在 processor-local 变量和 processor-global 变量的传值过程中。
稍加回溯：
void ESolver_FP::Init(Input& inp, UnitCell& cell)
@@ -968,7 +968,7 @@ ## 实空间：PW_Basis::distribute_r()
+实空间：PW_Basis::distribute_r()
❗Attention
注意，此时实际调用的也是 PW_Basis_Big 而非 PW_Basis 的 distribute_r() 函数。
@@ -1011,8 +1011,8 @@ {
....
No results matching "
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diff --git a/_book/develop-path1.html b/_book/develop-path1.html
index 1de92b86..d41c1be3 100644
--- a/_book/develop-path1.html
+++ b/_book/develop-path1.html
@@ -1112,8 +1112,8 @@ <
Input_Conv::Convert()
这个函数实现了从 Input 类对象的数据成员到 GlobalV 和 GlobalC 等全局变量集合的转换。相当于从 Input 到 GlobalV 和 GlobalC，以及其他直接的类的参数上载：
-其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
+其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
void Input_Conv::Convert(void)
{
....
@@ -1308,7 +1308,7 @@
不要忘记我们已经完成 Driver::reading() 函数内容，到达 Driver::atomic_world()。这一点从本文档设置的分级目录中也可以看得到。
-cppvoid Driver::init()
+void Driver::init()
{
this->reading();
this->atomic_world(); // <- here!
@@ -1518,7 +1518,7 @@ 从 SIAB 到 ABACUS（一）：准备工作（施工中 🚧）
下篇：Introduction to ABACUS: Path to PW calculation - Part 2
@@ -1562,7 +1562,7 @@ No results matching "
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V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","attributes":{},"skip":false,"key":"1.1.15.5"},{"backlink":"abacus-surface6.html#fig1.1.16.1","level":"1.1.16","list_caption":"Figure: 一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","alt":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","nro":14,"url":"picture/fig_surface6-1.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","attributes":{},"skip":false,"key":"1.1.16.1"},{"backlink":"abacus-surface6.html#fig1.1.16.2","level":"1.1.16","list_caption":"Figure: 静电势（Electrostatic Potential）沿超胞Z轴变化图","alt":"静电势（Electrostatic Potential）沿超胞Z轴变化图","nro":15,"url":"picture/fig_surface6-2.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"静电势（Electrostatic Potential）沿超胞Z轴变化图","attributes":{},"skip":false,"key":"1.1.16.2"},{"backlink":"develop-path4.html#fig1.2.9.1","level":"1.2.9","list_caption":"Figure: ","alt":" 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example","attributes":{},"skip":false,"key":"1.2.10.5"}]},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"develop-path1.md","mtime":"2023-10-04T14:18:52.079Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-10-04T15:29:41.868Z"},"basePath":".","book":{"language":""}});
});
diff --git a/_book/develop-path2.html b/_book/develop-path2.html
index 191dfe74..d829579b 100644
--- a/_book/develop-path2.html
+++ b/_book/develop-path2.html
@@ -1028,7 +1028,7 @@ // a(i) is lattice vector
}
-我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
+我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
UnitCell::read_atom_positions()
🔧重构思考
@@ -1042,7 +1042,7 @@
::
GlobalFunc::READ_VALUE( ifpos, Coordinate);
STRU 第二行指定坐标类型，被读取为 UnitCell::Coordinate。UnitCell::Coordinate 在 STRU 里有不同选项，⚙ 决定原子的具体位置和单位：
-if(Coordinate != "Cartesian"
+ if(Coordinate != "Cartesian"
&& Coordinate != "Direct"
&& Coordinate != "Cartesian_angstrom"
&& Coordinate != "Cartesian_au"
@@ -1092,7 +1092,7 @@ int na = 0;
+ int na = 0;
this->nat = 0;
assert(ntype>0);
for (int it = 0;it < ntype; it++)
@@ -1105,7 +1105,7 @@ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
bool sequence_match = false;
for(int it2=0; it2<ntype; it2++)
{
@@ -1121,7 +1121,7 @@ }
读取当前原子类型的 starting_magnetization、原子总数 na
-ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
...
ModuleBase::GlobalFunc::READ_VALUE(ifpos, na);
this->atoms[it].na = na;
@@ -1149,17 +1149,17 @@ [
it].m_loc_ = new ModuleBase::Vector3<double>[na];
⚙ 然后在 ATOMIC_POSITIONS 中读取：
-atoms[it].mass = this->atom_mass[it];
+ atoms[it].mass = this->atom_mass[it];
❗ 此处的 atoms[it].mass 与 this->atom_mass[it] 的用法与 atomis[it].label 与 this->atom_label[it] 不同：传值 vs 核对。
接下来读取类中每个原子的速度信息，在做分子动力学模拟的时候可能需要用到：
-for (int ia = 0;ia < na; ia++)
+ for (int ia = 0;ia < na; ia++)
{
ifpos >> v.x >> v.y >> v.z;
然而，当前 STRU 文件在 ATOMIC_POSITIONS 的设计比较复杂，其可以包括任何一组 atom-specific 数据，且数量和顺序均不受限制，这导致判断条件变得复杂，详见 module_cell/read_atoms.cpp:line 536 - 567（link）。
atoms[it].mag 的赋值并非直接读取：
-else if ( tmpid == "mag" || tmpid == "magmom")
+ else if ( tmpid == "mag" || tmpid == "magmom")
{
set_element_mag_zero = true;
double tmpamg=0; ifpos >> tmpamg;
@@ -1185,7 +1185,7 @@ }
⚙ 若 mag/magmom 后有一个值，则读取其值赋给 atoms[it]::mag[ia]，将 input_vec_mag 置为 false，若有三个值，则三个值依次被传入 atoms[it].m_loc_[ia].x, atoms[it].m_loc_[ia].y 和 atoms[it].m_loc_[ia].z，并将 input_vec_mag 置为 true，之后其向量模长为 atoms[it]::mag[ia]，然后在使用 angle1, angle2 来重新生成 mag。
-if(GlobalV::NSPIN==4)
+ if(GlobalV::NSPIN==4)
{
if(GlobalV::NONCOLIN)
{
@@ -1227,7 +1227,7 @@ pw.x input description
ABACUS 对 nspin=4 情况的参数处理：
//module_io/input_conv.cpp line 376
if (INPUT.noncolin || INPUT.lspinorb)
@@ -1312,7 +1312,7 @@
UnitCell::setup_cell(): the rest, and an example of backtracking unclear variable
离开 STRU 文件的解析部分，接下来计算了初始磁化强度：
-//after read STRU, calculate initial total magnetization when NSPIN=2
+ //after read STRU, calculate initial total magnetization when NSPIN=2
if(GlobalV::NSPIN == 2 && !GlobalV::TWO_EFERMI)
{
for(int it = 0;it<this->ntype; it++)
@@ -1326,31 +1326,25 @@ if (std::abs(INPUT.nupdown) > 1e-6)
- {
- GlobalV::TWO_EFERMI = true;
- GlobalV::nupdown = INPUT.nupdown;
- }
-
-因此 GlobalV::TWO_EFERMI 变量实际依赖于 INPUT.nupdown。
-
-- 接下来在
module_io/input.cpp 中寻找含 INPUT.nupdown 的 if(strcmp(...)) 单元，查看在 INPUT 文件中是何参数赋予其具体值：
-
-else if (strcmp("nupdown", word) == 0)
+在 module_io/input_conv.cpp 中寻找该变量，是何变量赋其值，发现： if (std::abs(INPUT.nupdown) > 1e-6)
{
- read_value(ifs, nupdown);
- }
+ GlobalV::TWO_EFERMI = true;
+ GlobalV::nupdown = INPUT.nupdown;
+ }
-即 INPUT.nupdown 在 INPUT 中也为 nupdown。接下来打开 Full keyword list 寻找其解释。
-
+ 因此 GlobalV::TWO_EFERMI 变量实际依赖于 INPUT.nupdown。
+接下来在 module_io/input.cpp 中寻找含 INPUT.nupdown 的 if(strcmp(...)) 单元，查看在 INPUT 文件中是何参数赋予其具体值： else if (strcmp("nupdown", word) == 0)
+ {
+ read_value(ifs, nupdown);
+ }
+
+即 INPUT.nupdown 在 INPUT 中也为 nupdown。接下来打开 Full keyword list 寻找其解释。
得到结果，即 nupdown 为 spin up 和 spin down 电子数量差值：
因此该部分逻辑为：若未使用 nupdown 来指定单电子数量，则对每种原子内每个原子，累加其 mag/magmom，即磁矩模长，赋予 GlobalV::nupdown。❗ 但对于两种方式均赋予，但值不一致的情况未进行处理。
接下来根据在 STRU 中读取的晶胞参数，计算晶胞体积，并计算倒空间矢量（在上篇中已经对 latvec, G, GT, GGT 有所介绍，invGGT 的意义也不言自明）：
-this->omega = std::abs( latvec.Det() ) * this->lat0 * lat0 * lat0 ;
+ this->omega = std::abs( latvec.Det() ) * this->lat0 * lat0 * lat0 ;
this->GT = latvec.Inverse();
this->G = GT.Transpose();
@@ -1442,7 +1436,7 @@ =
static_cast<ModulePW::PW_Basis_Big*>(pw_rho);
对于 ESolver 本身，其指针对象 p_esolver 实际上也有类似操作：
-//Some API to operate E_Solver
+ //Some API to operate E_Solver
void init_esolver(ESolver*& p_esolver)
{
//determine type of esolver based on INPUT information
@@ -1907,7 +1901,7 @@ Introduction to ABACUS: Path to PW calculation - Part 1
下篇：Introduction to ABACUS: Path to PW calculation - Part 3
@@ -1951,7 +1945,7 @@ No results matching "
var gitbook = gitbook || [];
gitbook.push(function() {
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采用PBE交换关联泛函和自旋极化得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出不加电场时，两个自旋方向的能带图几乎一样，都有带隙。","alt":"采用PBE交换关联泛函和自旋极化得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出不加电场时，两个自旋方向的能带图几乎一样，都有带隙。","nro":12,"url":"picture/fig_surface5-4.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"采用PBE交换关联泛函和自旋极化得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出不加电场时，两个自旋方向的能带图几乎一样，都有带隙。","attributes":{},"skip":false,"key":"1.1.15.4"},{"backlink":"abacus-surface5.html#fig1.1.15.5","level":"1.1.15","list_caption":"Figure: 采用PBE交换关联泛函和自旋极化，再给体系加上0.1 V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","alt":"采用PBE交换关联泛函和自旋极化，再给体系加上0.1 V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","nro":13,"url":"picture/fig_surface5-5.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"采用PBE交换关联泛函和自旋极化，再给体系加上0.1 V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","attributes":{},"skip":false,"key":"1.1.15.5"},{"backlink":"abacus-surface6.html#fig1.1.16.1","level":"1.1.16","list_caption":"Figure: 一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","alt":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","nro":14,"url":"picture/fig_surface6-1.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","attributes":{},"skip":false,"key":"1.1.16.1"},{"backlink":"abacus-surface6.html#fig1.1.16.2","level":"1.1.16","list_caption":"Figure: 静电势（Electrostatic Potential）沿超胞Z轴变化图","alt":"静电势（Electrostatic Potential）沿超胞Z轴变化图","nro":15,"url":"picture/fig_surface6-2.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"静电势（Electrostatic Potential）沿超胞Z轴变化图","attributes":{},"skip":false,"key":"1.1.16.2"},{"backlink":"develop-path4.html#fig1.2.9.1","level":"1.2.9","list_caption":"Figure: ","alt":" ","nro":16,"url":"picture/fig_path4-1.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":" ","attributes":{},"skip":false,"key":"1.2.9.1"},{"backlink":"develop-path4.html#fig1.2.9.2","level":"1.2.9","list_caption":"Figure: PW_Basis::distribute_r()：设一个pool中有5个processors","alt":"PW_Basis::distribute_r()：设一个pool中有5个processors","nro":17,"url":"picture/fig_path4-2.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"PW_Basis::distribute_r()：设一个pool中有5个processors","attributes":{},"skip":false,"key":"1.2.9.2"},{"backlink":"develop-path4.html#fig1.2.9.3","level":"1.2.9","list_caption":"Figure: this->count_pw_st(st_length2D, st_bottom2D)","alt":"this->count_pw_st(st_length2D, st_bottom2D)","nro":18,"url":"picture/fig_path4-3.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"this->count_pw_st(st_length2D, st_bottom2D)","attributes":{},"skip":false,"key":"1.2.9.3"},{"backlink":"develop-path5.html#fig1.2.10.1","level":"1.2.10","list_caption":"Figure: 善用Ctrl+F","alt":"善用Ctrl+F","nro":19,"url":"picture/fig_path5-9.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"善用Ctrl+F","attributes":{},"skip":false,"key":"1.2.10.1"},{"backlink":"develop-path5.html#fig1.2.10.2","level":"1.2.10","list_caption":"Figure: klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","alt":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","nro":20,"url":"picture/fig_path5-10.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","attributes":{},"skip":false,"key":"1.2.10.2"},{"backlink":"develop-path5.html#fig1.2.10.3","level":"1.2.10","list_caption":"Figure: klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","alt":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","nro":21,"url":"picture/fig_path5-11.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","attributes":{},"skip":false,"key":"1.2.10.3"},{"backlink":"develop-path5.html#fig1.2.10.4","level":"1.2.10","list_caption":"Figure: 1-dimensional example","alt":"1-dimensional example","nro":22,"url":"picture/fig_path5-12.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"1-dimensional example","attributes":{},"skip":false,"key":"1.2.10.4"},{"backlink":"develop-path5.html#fig1.2.10.5","level":"1.2.10","list_caption":"Figure: 2-dimensional example","alt":"2-dimensional example","nro":23,"url":"picture/fig_path5-13.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"2-dimensional example","attributes":{},"skip":false,"key":"1.2.10.5"}]},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"develop-path2.md","mtime":"2023-10-04T14:37:12.149Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-10-04T15:29:41.868Z"},"basePath":".","book":{"language":""}});
});
diff --git a/_book/develop-path3.html b/_book/develop-path3.html
index b8de33d9..09176394 100644
--- a/_book/develop-path3.html
+++ b/_book/develop-path3.html
@@ -750,11 +750,11 @@ Driver
-Driver::atomic_world()
-Driver::driver_run()
-多层继承：Init() functions in esolver class
-Trigger: ESolver_FP::Init()
+Driver
+Driver::atomic_world()
+Driver::driver_run()
+多层继承：Init() functions in esolver class
+Trigger: ESolver_FP::Init()
承接上篇中已经导入的结构信息，以及了解到构造函数及其伴随的变量初始化和 ABACUS 里应用到的 C++ 多态编程，接下来即将（逐渐）步入 ABACUS 的核心内容。我们暂时跳过位于 source/driver_run.cpp:driver_run() 的：
// 3. For these two types of calculations
// nothing else need to be initialized
@@ -830,14 +830,14 @@ }
同理，ESolver_KS 的数据成员，也被 ESolver_KS_PW 继承。ESolver_FP::Init() 首先调用 UnitCell::read_pseudo() 函数进行赝势文件读取，而将赝势文件读取任务放在 FP 层级下，也暗示对于 ABACUS 的第一性原理方法实现来讲，都需要使用赝势。
-Pseudopotential import: UnitCell::read_pseudo()
+Pseudopotential import: UnitCell::read_pseudo()
void UnitCell::read_pseudo(std::ofstream &ofs)
{
read_cell_pseudopots(GlobalV::global_pseudo_dir, ofs);
在解读赝势文件读取功能之前，首先需要对赝势文件的结构和信息做一定程度的了解。
-# ONCV pseudopotential file
-## Section 0: Norm-conserving conditions, generation of pseudopotential and header of exact UPF file
+ONCV pseudopotential file
+Section 0: Norm-conserving conditions, generation of pseudopotential and header of exact UPF file
赝势的意义不言自明，其中模守恒赝势需满足如下条件：
- （赝势得到的能级和全电子方法求解的能级一样，这里 ps 代表 pseudopotentials）
@@ -852,7 +852,7 @@ V_l(r)=\frac{1}{\phi^\text{ps}_l(r)}[\epsilon^\text{ps}_l-\frac{\hbar^2}{2m}\frac{l(l+1)}{r^2}+\frac{\hbar^2}{2m}\frac{d^2}{dr^2}]\phi^\text{ps}_l(r)，解得。
- 扣除中 Hartree、xc 部分，得到：。
-更多细节见
+更多细节见：www.tcm.phy.cam.ac.uk
<UPF version="2.0.1">
<PP_INFO>
<!-- omitted information here -->
@@ -865,8 +865,8 @@ <!-- -->
从 UPF 文件（注意 UPF 文件也有不同的版本，目前 ABACUS 都支持，若有不支持的，可以提 Github 的 issues 进行讨论）开始，截止到 <PP_HEADER> 之前，提供了赝势文件的作者信息，引用信息以及生成赝势文件所使用的程序和相应输入文件，并附带输入文件参数中的解释。由于此块内容对实际计算并不起作用，因此暂时略过。
-## Section 1:
-<PP_HEADER
+Section 1:
+ <PP_HEADER
generated="Generated using ONCVPSP code by D. R. Hamann" author="Martin Schlipf and Francois Gygi"
date="150105" comment=""
element="Al"
@@ -890,8 +890,8 @@ number_of_proj
="4"/>
<PP_HEADER> 部分尽管已经位于所谓“not human readable”区域，但也并非如此。这部分“标签”（HTML 语境）/block 实际上包含了众多精简过的信息，如元素名称（element）、赝势类型（pseudo_type，模守恒，norm-conserving，NC），相对论效应（relativistic），是否为超软赝势等等信息。当前 Al 理论上其原子序数 13，因此有 13 个电子，但此处 z_valence 参数为 11，即有两个 1s 电子被赝化，只留下 2s, 2p, 3s, 3p 电子共 2+6+2+1 个。对于某些元素，甚至有大核赝势与小核赝势之分，根据赝化电子数量不同进行区分。显而易见地，赝化电子数量越多，则计算量越小，但计算结果的精确程度可能更低。
-## Section 2:
-<PP_MESH>
+Section 2:
+ <PP_MESH>
<PP_R type="real" size=" 602" columns="8">
0.0000 0.0100 0.0200 0.0300 0.0400 0.0500 0.0600 0.0700
<!-- omitted information here -->
@@ -907,8 +907,8 @@ </PP_MESH>
这部分开始出现了关于实空间格点相关量的定义。在 tag 中不仅指定数据类型为实数，也指定当前数据的长度（size），以及数据存储的列数（columns = 8）。PP_R 为格点坐标，PP_RAB 则为格点间距。
-## Section 3:
-<PP_LOCAL type="real" size=" 602" columns="4">
+Section 3:
+ <PP_LOCAL type="real" size=" 602" columns="4">
-4.5793174225E+01 -4.5788454271E+01 -4.5774276797E+01 -4.5750659428E+01
<!-- omitted information here -->
-3.6912752197E+00 -3.6850921941E+00 -3.6789298138E+00 -3.6727880140E+00
@@ -917,8 +917,8 @@ <PP_LOCAL>
部分开始，正式开始写入赝势的具体数值，建立在 <PP_R> 和 <PP_RAB> 所描述的实空间格点上。。<PP_LOCAL> 正是赝势的局域势部分。
-## Section 4:
-<PP_NONLOCAL>
+Section 4:
+ <PP_NONLOCAL>
<PP_BETA.1
type="real"
size=" 602"
@@ -938,8 +938,8 @@ cutoff_radius_index
=" 246" cutoff_radius=" 2.4500000000E+00" >
<!-- omitted information here -->
</PP_BETA.2>
- <PP_BETA.3 type="real" size=" 602" columns="4" index="3" angular_momentum="1"<strong>
-</strong> cutoff_radius_index=" 246" cutoff_radius=" 2.4500000000E+00" >
+ <PP_BETA.3 type="real" size=" 602" columns="4" index="3" angular_momentum="1"
+ cutoff_radius_index=" 246" cutoff_radius=" 2.4500000000E+00" >
<!-- omitted information here -->
</PP_BETA.3>
<PP_BETA.4 type="real" size=" 602" columns="4" index="4" angular_momentum="1"
@@ -956,7 +956,7 @@ \hat{V}^\text{NL}=\sum_{ij}{|\beta_i\rangle D_{ij}\langle\beta_j|}。其中一般被称为非局域势投影子（projector）。
-## Section 5: and
+Section 5: and
<PP_PSWFC>
</PP_PSWFC>
<PP_RHOATOM type="real" size=" 602" columns="4">
@@ -975,7 +975,7 @@ |\beta\rangle和 pswfc 已经乘径向坐标。
-# UnitCell::read_cell_pseudopots()
+UnitCell::read_cell_pseudopots()
link to Github -> link
void UnitCell::read_cell_pseudopots(const std::string &pp_dir, std::ofstream &log)
{
@@ -1030,7 +1030,7 @@ while (ifs.good())
+ while (ifs.good())
{
ifs >> dummy;
if(dummy=="<PP_HEADER>")
@@ -1044,7 +1044,7 @@ if ( ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_MESH>") )
+ if ( ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_MESH>") )
{
read_pseudo_mesh(ifs);
ModuleBase::GlobalFunc::SCAN_END(ifs, "</PP_MESH>");
@@ -1052,7 +1052,7 @@ if (this->nlcc)
+ if (this->nlcc)
{
ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_NLCC>");
read_pseudo_nlcc(ifs);
@@ -1061,12 +1061,12 @@ ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_LOCAL>");
+ ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_LOCAL>");
read_pseudo_local(ifs);
ModuleBase::GlobalFunc::SCAN_END(ifs, "</PP_LOCAL>");
与 类似的还有 , , , 从 则可以读取旋轨耦合相关信息：
-if (has_so)
+ if (has_so)
{
ModuleBase::GlobalFunc::SCAN_BEGIN (ifs,"<PP_ADDINFO>");
read_pseudo_so (ifs);
@@ -1140,7 +1140,7 @@ if(error==0)
+ if(error==0)
{
if(this->atoms[i].flag_empty_element) upf.set_empty_element();
error_ap = upf.average_p(GlobalV::soc_lambda);
@@ -1148,7 +1148,7 @@ if(GlobalV::MY_RANK==0)
+ if(GlobalV::MY_RANK==0)
{
atoms[i].ncpp.set_pseudo_nc( upf );
....
@@ -1178,7 +1178,7 @@ }
该函数属于类 pseudo_nc，而 pseudo_nc 对象为 atom 的数据成员，atoms 则为 UnitCell 的数据成员。pseudo_nc::set_pseudo_h()，pseudo_nc::set_pseudo_atom 和 pseudo_nc::set_pseudo_vl 的内容在此省略，但其分别为将 Hamilton, 原子性质和 Vlocal 相关数据从 upf 对象拷贝。之后(1)使用 lll 刷新为 upf 对象的 projectors 的角动量，然后计算出磁角动量区分时的 projector 个数。(2)取所有 projector 衰减到 0 时候的最大最普适半径。
-# 赝势信息后处理
+赝势信息后处理
回到 module_cell/unitcell.cpp line 663，接下来为每个原子创建目录，在目录中写 [原子label].NONLOCAL 文件。[label].NONLOCAL 文件中内容包含 <HEADER>, <DIJ> 和 <PP_BETA> 三个 tag。
<HEADER> 中包含内容：
ofs << "<HEADER>" << std::endl;
@@ -1222,21 +1222,61 @@ }
ofs << "</PP_BETA>" << std::endl;
-# 赝势信息分发：UnitCell::bcast_unitcell2(void)
+赝势信息分发：UnitCell::bcast_unitcell2(void)
#ifdef __MPI
+接下来对赝势信息进行MPI进程（processor）间的分发：
+#ifdef __MPI
+ bcast_unitcell2();
+#endif
+
+// module_cell/unitcell.cpp:bcast_unitcell2()
+void UnitCell::bcast_unitcell2(void)
+{
+ for (int i = 0; i < ntype; i++)
+ {
+ atoms[i].bcast_atom2();
+ }
+ return;
+}
+
+// module_cell/atom_spec.cpp:Atom::bcast_atom2()
+void Atom::bcast_atom2()
+{
+ this->ncpp.bcast_atom_pseudo();
+}
+
+// module_cell/atom_pseudo.cpp::Atom_pseudo::bcast_atom_pseudo()
+void Atom_pseudo::bcast_atom_pseudo(void)
+{
+....
+ Parallel_Common::bcast_int( lmax );
+....
+ Parallel_Common::bcast_double( etotps );
+....
+ Parallel_Common::bcast_bool( tvanp );
+....
+ Parallel_Common::bcast_string( psd );
+....
+ // below two 'bcast_double' lines of codes seem to have bugs,
+ // on some computers, the code will stuck here for ever.
+ // mohan note 2021-04-28
+ Parallel_Common::bcast_double( dion.c , nbeta * nbeta);
+ Parallel_Common::bcast_double( betar.c, nr * nc );
+}
+
#endif
-# 赝势信息核对
+赝势信息核对
接下来跨原子种类检验泛函是否一致：
-for(int it=0; it<ntype; it++)
+ for(int it=0; it<ntype; it++)
{
if(atoms[0].ncpp.xc_func !=atoms[it].ncpp.xc_func)
{
-# STRU 结构检查：UnitCell::check_structure()
+STRU 结构检查：UnitCell::check_structure()
检验结构中任意两原子之间距离是否大于其固定倍数（<1）的共价半径和，
-check_structure(GlobalV::MIN_DIST_COEF);
+ check_structure(GlobalV::MIN_DIST_COEF);
-# 计算轨道数：UnitCell::cal_natomwfc()
+计算轨道数：UnitCell::cal_natomwfc()
UnitCell::cal_natomwfc() 函数计算所有种类的原子轨道数量加和，对于非 nspin=4，即非 soc（自旋轨道耦合）情况，角量子数 l 和 s 非耦合，l 单独可以作为好的量子数来区分量子态，因此对于每个赝势中定义的 wfc，若其对应 occupation 大于等于 0（即有效 wfc），则对应于其角量子数 l，轨道数量增加 2l+1，即计数其磁量子数 m，也相当于对 alpha 和 beta spin 的单独计数。对于 nspin=4 的情况，若考虑 soc，则轨道数对 j=l+s 的情况，当前原子种类当前角量子数对应轨道数量记为 2l+1+1，否则为 2l+1。对于非 soc 但 nspin=4，当前原子种类轨道当前角量子数对应轨道数量记(2l+1)*2：
void UnitCell::cal_natomwfc(std::ofstream &log)
{
@@ -1291,9 +1331,9 @@ 计算跨原子种类最大角量子数 UnitCell::lmax 和某 l 对应最大 zeta 数 UnitCell::nmax，以及跨原子种类的类内 zeta 数总和最大值 UnitCell::nmax_total
寻找赝势中最大角量子数 UnitCell::lmax_ppwf。
-# 价电子数核对
+价电子数核对
核对赝势中定义的价电子数与 ABACUS 预置库中原子的最小价电子数
-# 获取最大格点数量：UnitCell::cal_meshx()
+获取最大格点数量：UnitCell::cal_meshx()
计算跨原子种类的最大格点数量，存储在 UnitCell::meshx 中，目前 ABACUS 代码中变量命名后缀 x 可能代表 max，正如之前看到 npwx 等。
至此，我们离开函数 UnitCell::read_pseudo()，回到 ModuleESolver::ESolver_FP::Init() 函数。
@@ -1304,7 +1344,7 @@ Introduction to ABACUS: Path to PW calculation - Part 2
下篇：Introduction to ABACUS: Path to PW calculation - Part 4
@@ -1348,7 +1388,7 @@ No results matching "
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V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","attributes":{},"skip":false,"key":"1.1.15.5"},{"backlink":"abacus-surface6.html#fig1.1.16.1","level":"1.1.16","list_caption":"Figure: 一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","alt":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","nro":14,"url":"picture/fig_surface6-1.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","attributes":{},"skip":false,"key":"1.1.16.1"},{"backlink":"abacus-surface6.html#fig1.1.16.2","level":"1.1.16","list_caption":"Figure: 静电势（Electrostatic Potential）沿超胞Z轴变化图","alt":"静电势（Electrostatic Potential）沿超胞Z轴变化图","nro":15,"url":"picture/fig_surface6-2.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"静电势（Electrostatic Potential）沿超胞Z轴变化图","attributes":{},"skip":false,"key":"1.1.16.2"},{"backlink":"develop-path4.html#fig1.2.9.1","level":"1.2.9","list_caption":"Figure: ","alt":" 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st_bottom2D)","attributes":{},"skip":false,"key":"1.2.9.3"},{"backlink":"develop-path5.html#fig1.2.10.1","level":"1.2.10","list_caption":"Figure: 善用Ctrl+F","alt":"善用Ctrl+F","nro":19,"url":"picture/fig_path5-9.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"善用Ctrl+F","attributes":{},"skip":false,"key":"1.2.10.1"},{"backlink":"develop-path5.html#fig1.2.10.2","level":"1.2.10","list_caption":"Figure: klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","alt":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","nro":20,"url":"picture/fig_path5-10.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","attributes":{},"skip":false,"key":"1.2.10.2"},{"backlink":"develop-path5.html#fig1.2.10.3","level":"1.2.10","list_caption":"Figure: klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","alt":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","nro":21,"url":"picture/fig_path5-11.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","attributes":{},"skip":false,"key":"1.2.10.3"},{"backlink":"develop-path5.html#fig1.2.10.4","level":"1.2.10","list_caption":"Figure: 1-dimensional example","alt":"1-dimensional example","nro":22,"url":"picture/fig_path5-12.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"1-dimensional example","attributes":{},"skip":false,"key":"1.2.10.4"},{"backlink":"develop-path5.html#fig1.2.10.5","level":"1.2.10","list_caption":"Figure: 2-dimensional example","alt":"2-dimensional example","nro":23,"url":"picture/fig_path5-13.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"2-dimensional 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diff --git a/_book/develop-path4.html b/_book/develop-path4.html
index 1840948c..2b9cddf9 100644
--- a/_book/develop-path4.html
+++ b/_book/develop-path4.html
@@ -750,14 +750,14 @@ Driver
-Driver::atomic_world()
-Driver::driver_run()
-多层继承：Init() functions in esolver class
-Trigger: ESolver_FP::Init()
-平面波格点初始化：PW_Basis:: initgrids()
+Driver
+Driver::atomic_world()
+Driver::driver_run()
+多层继承：Init() functions in esolver class
+Trigger: ESolver_FP::Init()
+平面波格点初始化：PW_Basis:: initgrids()
完成了 INPUT 和 STRU，以及赝势文件的读取环节，接下来我们来到平面波的初始化设置相关部分。
-void ESolver_FP::Init(Input& inp, UnitCell& cell)
+ void ESolver_FP::Init(Input& inp, UnitCell& cell)
{
....
if (inp.nx * inp.ny * inp.nz == 0)
@@ -782,7 +782,7 @@ virtual void initgrids(const double lat0_in,const ModuleBase::Matrix3 latvec_in,
+ virtual void initgrids(const double lat0_in,const ModuleBase::Matrix3 latvec_in,
const double gridecut)
{
// generation of nx, ny and nz are omitted here
@@ -868,7 +868,7 @@ }
❗ 注意：这里还完成了倒空间格点数量 fftnx, fftny 和 fftnz 的赋值。因为 FFT 变换前后的格点数量一般相同，因此 fftnx = nx，fftny = ny，...。
-
+图 1. 然后对平面波在 MPI 进程间进行分发：
//module_esolver/esolver_fp.cpp
void ESolver_FP::Init(Input& inp, UnitCell& cell)
@@ -889,9 +889,9 @@ ::
timer::tick(this->classname, "setuptransform");
}
-PW_Basis::setuptransform()（link）
-# 并行机制简述
-## 并行池
+PW_Basis::setuptransform()（link）
+并行机制简述
+并行池
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diff --git a/_book/develop-path1.html b/_book/develop-path1.html
index 1de92b86..d41c1be3 100644
--- a/_book/develop-path1.html
+++ b/_book/develop-path1.html
@@ -1112,8 +1112,8 @@ <
Input_Conv::Convert()
这个函数实现了从 Input 类对象的数据成员到 GlobalV 和 GlobalC 等全局变量集合的转换。相当于从 Input 到 GlobalV 和 GlobalC，以及其他直接的类的参数上载：
-其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
+其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
void Input_Conv::Convert(void)
{
....
@@ -1308,7 +1308,7 @@
不要忘记我们已经完成 Driver::reading() 函数内容，到达 Driver::atomic_world()。这一点从本文档设置的分级目录中也可以看得到。
-cppvoid Driver::init()
+void Driver::init()
{
this->reading();
this->atomic_world(); // <- here!
@@ -1518,7 +1518,7 @@ 从 SIAB 到 ABACUS（一）：准备工作（施工中 🚧）
下篇：Introduction to ABACUS: Path to PW calculation - Part 2
@@ -1562,7 +1562,7 @@ No results matching "
var gitbook = gitbook || [];
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index 191dfe74..d829579b 100644
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@@ -1028,7 +1028,7 @@ // a(i) is lattice vector
}
-我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
+我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
UnitCell::read_atom_positions()
🔧重构思考
@@ -1042,7 +1042,7 @@
::
GlobalFunc::READ_VALUE( ifpos, Coordinate);
STRU 第二行指定坐标类型，被读取为 UnitCell::Coordinate。UnitCell::Coordinate 在 STRU 里有不同选项，⚙ 决定原子的具体位置和单位：
-if(Coordinate != "Cartesian"
+ if(Coordinate != "Cartesian"
&& Coordinate != "Direct"
&& Coordinate != "Cartesian_angstrom"
&& Coordinate != "Cartesian_au"
@@ -1092,7 +1092,7 @@ int na = 0;
+ int na = 0;
this->nat = 0;
assert(ntype>0);
for (int it = 0;it < ntype; it++)
@@ -1105,7 +1105,7 @@ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
bool sequence_match = false;
for(int it2=0; it2<ntype; it2++)
{
@@ -1121,7 +1121,7 @@ }
读取当前原子类型的 starting_magnetization、原子总数 na
-ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
...
ModuleBase::GlobalFunc::READ_VALUE(ifpos, na);
this->atoms[it].na = na;
@@ -1149,17 +1149,17 @@ [
it].m_loc_ = new ModuleBase::Vector3<double>[na];
⚙ 然后在 ATOMIC_POSITIONS 中读取：
-atoms[it].mass = this->atom_mass[it];
+ atoms[it].mass = this->atom_mass[it];
❗ 此处的 atoms[it].mass 与 this->atom_mass[it] 的用法与 atomis[it].label 与 this->atom_label[it] 不同：传值 vs 核对。
接下来读取类中每个原子的速度信息，在做分子动力学模拟的时候可能需要用到：
-for (int ia = 0;ia < na; ia++)
+ for (int ia = 0;ia < na; ia++)
{
ifpos >> v.x >> v.y >> v.z;
然而，当前 STRU 文件在 ATOMIC_POSITIONS 的设计比较复杂，其可以包括任何一组 atom-specific 数据，且数量和顺序均不受限制，这导致判断条件变得复杂，详见 module_cell/read_atoms.cpp:line 536 - 567（link）。
atoms[it].mag 的赋值并非直接读取：
-else if ( tmpid == "mag" || tmpid == "magmom")
+ else if ( tmpid == "mag" || tmpid == "magmom")
{
set_element_mag_zero = true;
double tmpamg=0; ifpos >> tmpamg;
@@ -1185,7 +1185,7 @@ }
⚙ 若 mag/magmom 后有一个值，则读取其值赋给 atoms[it]::mag[ia]，将 input_vec_mag 置为 false，若有三个值，则三个值依次被传入 atoms[it].m_loc_[ia].x, atoms[it].m_loc_[ia].y 和 atoms[it].m_loc_[ia].z，并将 input_vec_mag 置为 true，之后其向量模长为 atoms[it]::mag[ia]，然后在使用 angle1, angle2 来重新生成 mag。
-if(GlobalV::NSPIN==4)
+ if(GlobalV::NSPIN==4)
{
if(GlobalV::NONCOLIN)
{
@@ -1227,7 +1227,7 @@ pw.x input description
ABACUS 对 nspin=4 情况的参数处理：
//module_io/input_conv.cpp line 376
if (INPUT.noncolin || INPUT.lspinorb)
@@ -1312,7 +1312,7 @@
UnitCell::setup_cell(): the rest, and an example of backtracking unclear variable
离开 STRU 文件的解析部分，接下来计算了初始磁化强度：
-//after read STRU, calculate initial total magnetization when NSPIN=2
+ //after read STRU, calculate initial total magnetization when NSPIN=2
if(GlobalV::NSPIN == 2 && !GlobalV::TWO_EFERMI)
{
for(int it = 0;it<this->ntype; it++)
@@ -1326,31 +1326,25 @@ if (std::abs(INPUT.nupdown) > 1e-6)
- {
- GlobalV::TWO_EFERMI = true;
- GlobalV::nupdown = INPUT.nupdown;
- }
-
-因此 GlobalV::TWO_EFERMI 变量实际依赖于 INPUT.nupdown。
-
-- 接下来在
module_io/input.cpp 中寻找含 INPUT.nupdown 的 if(strcmp(...)) 单元，查看在 INPUT 文件中是何参数赋予其具体值：
-
-else if (strcmp("nupdown", word) == 0)
+在 module_io/input_conv.cpp 中寻找该变量，是何变量赋其值，发现： if (std::abs(INPUT.nupdown) > 1e-6)
{
- read_value(ifs, nupdown);
- }
+ GlobalV::TWO_EFERMI = true;
+ GlobalV::nupdown = INPUT.nupdown;
+ }
-即 INPUT.nupdown 在 INPUT 中也为 nupdown。接下来打开 Full keyword list 寻找其解释。
-
+ 因此 GlobalV::TWO_EFERMI 变量实际依赖于 INPUT.nupdown。
+接下来在 module_io/input.cpp 中寻找含 INPUT.nupdown 的 if(strcmp(...)) 单元，查看在 INPUT 文件中是何参数赋予其具体值： else if (strcmp("nupdown", word) == 0)
+ {
+ read_value(ifs, nupdown);
+ }
+
+即 INPUT.nupdown 在 INPUT 中也为 nupdown。接下来打开 Full keyword list 寻找其解释。
得到结果，即 nupdown 为 spin up 和 spin down 电子数量差值：
因此该部分逻辑为：若未使用 nupdown 来指定单电子数量，则对每种原子内每个原子，累加其 mag/magmom，即磁矩模长，赋予 GlobalV::nupdown。❗ 但对于两种方式均赋予，但值不一致的情况未进行处理。
接下来根据在 STRU 中读取的晶胞参数，计算晶胞体积，并计算倒空间矢量（在上篇中已经对 latvec, G, GT, GGT 有所介绍，invGGT 的意义也不言自明）：
-this->omega = std::abs( latvec.Det() ) * this->lat0 * lat0 * lat0 ;
+ this->omega = std::abs( latvec.Det() ) * this->lat0 * lat0 * lat0 ;
this->GT = latvec.Inverse();
this->G = GT.Transpose();
@@ -1442,7 +1436,7 @@ =
static_cast<ModulePW::PW_Basis_Big*>(pw_rho);
对于 ESolver 本身，其指针对象 p_esolver 实际上也有类似操作：
-//Some API to operate E_Solver
+ //Some API to operate E_Solver
void init_esolver(ESolver*& p_esolver)
{
//determine type of esolver based on INPUT information
@@ -1907,7 +1901,7 @@ Introduction to ABACUS: Path to PW calculation - Part 1
下篇：Introduction to ABACUS: Path to PW calculation - Part 3
@@ -1951,7 +1945,7 @@ No results matching "
var gitbook = gitbook || [];
gitbook.push(function() {
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st_bottom2D)","attributes":{},"skip":false,"key":"1.2.9.3"},{"backlink":"develop-path5.html#fig1.2.10.1","level":"1.2.10","list_caption":"Figure: 善用Ctrl+F","alt":"善用Ctrl+F","nro":19,"url":"picture/fig_path5-9.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"善用Ctrl+F","attributes":{},"skip":false,"key":"1.2.10.1"},{"backlink":"develop-path5.html#fig1.2.10.2","level":"1.2.10","list_caption":"Figure: klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","alt":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","nro":20,"url":"picture/fig_path5-10.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","attributes":{},"skip":false,"key":"1.2.10.2"},{"backlink":"develop-path5.html#fig1.2.10.3","level":"1.2.10","list_caption":"Figure: klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","alt":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","nro":21,"url":"picture/fig_path5-11.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","attributes":{},"skip":false,"key":"1.2.10.3"},{"backlink":"develop-path5.html#fig1.2.10.4","level":"1.2.10","list_caption":"Figure: 1-dimensional example","alt":"1-dimensional example","nro":22,"url":"picture/fig_path5-12.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"1-dimensional example","attributes":{},"skip":false,"key":"1.2.10.4"},{"backlink":"develop-path5.html#fig1.2.10.5","level":"1.2.10","list_caption":"Figure: 2-dimensional example","alt":"2-dimensional example","nro":23,"url":"picture/fig_path5-13.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"2-dimensional example","attributes":{},"skip":false,"key":"1.2.10.5"}]},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"develop-path2.md","mtime":"2023-10-04T14:37:12.149Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-10-04T15:29:41.868Z"},"basePath":".","book":{"language":""}});
});
diff --git a/_book/develop-path3.html b/_book/develop-path3.html
index b8de33d9..09176394 100644
--- a/_book/develop-path3.html
+++ b/_book/develop-path3.html
@@ -750,11 +750,11 @@ Driver
-Driver::atomic_world()
-Driver::driver_run()
-多层继承：Init() functions in esolver class
-Trigger: ESolver_FP::Init()
+Driver
+Driver::atomic_world()
+Driver::driver_run()
+多层继承：Init() functions in esolver class
+Trigger: ESolver_FP::Init()
承接上篇中已经导入的结构信息，以及了解到构造函数及其伴随的变量初始化和 ABACUS 里应用到的 C++ 多态编程，接下来即将（逐渐）步入 ABACUS 的核心内容。我们暂时跳过位于 source/driver_run.cpp:driver_run() 的：
// 3. For these two types of calculations
// nothing else need to be initialized
@@ -830,14 +830,14 @@ }
同理，ESolver_KS 的数据成员，也被 ESolver_KS_PW 继承。ESolver_FP::Init() 首先调用 UnitCell::read_pseudo() 函数进行赝势文件读取，而将赝势文件读取任务放在 FP 层级下，也暗示对于 ABACUS 的第一性原理方法实现来讲，都需要使用赝势。
-Pseudopotential import: UnitCell::read_pseudo()
+Pseudopotential import: UnitCell::read_pseudo()
void UnitCell::read_pseudo(std::ofstream &ofs)
{
read_cell_pseudopots(GlobalV::global_pseudo_dir, ofs);
在解读赝势文件读取功能之前，首先需要对赝势文件的结构和信息做一定程度的了解。
-# ONCV pseudopotential file
-## Section 0: Norm-conserving conditions, generation of pseudopotential and header of exact UPF file
+ONCV pseudopotential file
+Section 0: Norm-conserving conditions, generation of pseudopotential and header of exact UPF file
赝势的意义不言自明，其中模守恒赝势需满足如下条件：
- （赝势得到的能级和全电子方法求解的能级一样，这里 ps 代表 pseudopotentials）
@@ -852,7 +852,7 @@ V_l(r)=\frac{1}{\phi^\text{ps}_l(r)}[\epsilon^\text{ps}_l-\frac{\hbar^2}{2m}\frac{l(l+1)}{r^2}+\frac{\hbar^2}{2m}\frac{d^2}{dr^2}]\phi^\text{ps}_l(r)，解得。
- 扣除中 Hartree、xc 部分，得到：。
-更多细节见
+更多细节见：www.tcm.phy.cam.ac.uk
<UPF version="2.0.1">
<PP_INFO>
<!-- omitted information here -->
@@ -865,8 +865,8 @@ <!-- -->
从 UPF 文件（注意 UPF 文件也有不同的版本，目前 ABACUS 都支持，若有不支持的，可以提 Github 的 issues 进行讨论）开始，截止到 <PP_HEADER> 之前，提供了赝势文件的作者信息，引用信息以及生成赝势文件所使用的程序和相应输入文件，并附带输入文件参数中的解释。由于此块内容对实际计算并不起作用，因此暂时略过。
-## Section 1:
-<PP_HEADER
+Section 1:
+ <PP_HEADER
generated="Generated using ONCVPSP code by D. R. Hamann" author="Martin Schlipf and Francois Gygi"
date="150105" comment=""
element="Al"
@@ -890,8 +890,8 @@ number_of_proj
="4"/>
<PP_HEADER> 部分尽管已经位于所谓“not human readable”区域，但也并非如此。这部分“标签”（HTML 语境）/block 实际上包含了众多精简过的信息，如元素名称（element）、赝势类型（pseudo_type，模守恒，norm-conserving，NC），相对论效应（relativistic），是否为超软赝势等等信息。当前 Al 理论上其原子序数 13，因此有 13 个电子，但此处 z_valence 参数为 11，即有两个 1s 电子被赝化，只留下 2s, 2p, 3s, 3p 电子共 2+6+2+1 个。对于某些元素，甚至有大核赝势与小核赝势之分，根据赝化电子数量不同进行区分。显而易见地，赝化电子数量越多，则计算量越小，但计算结果的精确程度可能更低。
-## Section 2:
-<PP_MESH>
+Section 2:
+ <PP_MESH>
<PP_R type="real" size=" 602" columns="8">
0.0000 0.0100 0.0200 0.0300 0.0400 0.0500 0.0600 0.0700
<!-- omitted information here -->
@@ -907,8 +907,8 @@ </PP_MESH>
这部分开始出现了关于实空间格点相关量的定义。在 tag 中不仅指定数据类型为实数，也指定当前数据的长度（size），以及数据存储的列数（columns = 8）。PP_R 为格点坐标，PP_RAB 则为格点间距。
-## Section 3:
-<PP_LOCAL type="real" size=" 602" columns="4">
+Section 3:
+ <PP_LOCAL type="real" size=" 602" columns="4">
-4.5793174225E+01 -4.5788454271E+01 -4.5774276797E+01 -4.5750659428E+01
<!-- omitted information here -->
-3.6912752197E+00 -3.6850921941E+00 -3.6789298138E+00 -3.6727880140E+00
@@ -917,8 +917,8 @@ <PP_LOCAL>
部分开始，正式开始写入赝势的具体数值，建立在 <PP_R> 和 <PP_RAB> 所描述的实空间格点上。。<PP_LOCAL> 正是赝势的局域势部分。
-## Section 4:
-<PP_NONLOCAL>
+Section 4:
+ <PP_NONLOCAL>
<PP_BETA.1
type="real"
size=" 602"
@@ -938,8 +938,8 @@ cutoff_radius_index
=" 246" cutoff_radius=" 2.4500000000E+00" >
<!-- omitted information here -->
</PP_BETA.2>
- <PP_BETA.3 type="real" size=" 602" columns="4" index="3" angular_momentum="1"<strong>
-</strong> cutoff_radius_index=" 246" cutoff_radius=" 2.4500000000E+00" >
+ <PP_BETA.3 type="real" size=" 602" columns="4" index="3" angular_momentum="1"
+ cutoff_radius_index=" 246" cutoff_radius=" 2.4500000000E+00" >
<!-- omitted information here -->
</PP_BETA.3>
<PP_BETA.4 type="real" size=" 602" columns="4" index="4" angular_momentum="1"
@@ -956,7 +956,7 @@ \hat{V}^\text{NL}=\sum_{ij}{|\beta_i\rangle D_{ij}\langle\beta_j|}。其中一般被称为非局域势投影子（projector）。
-## Section 5: and
+Section 5: and
<PP_PSWFC>
</PP_PSWFC>
<PP_RHOATOM type="real" size=" 602" columns="4">
@@ -975,7 +975,7 @@ |\beta\rangle和 pswfc 已经乘径向坐标。
-# UnitCell::read_cell_pseudopots()
+UnitCell::read_cell_pseudopots()
link to Github -> link
void UnitCell::read_cell_pseudopots(const std::string &pp_dir, std::ofstream &log)
{
@@ -1030,7 +1030,7 @@ while (ifs.good())
+ while (ifs.good())
{
ifs >> dummy;
if(dummy=="<PP_HEADER>")
@@ -1044,7 +1044,7 @@ if ( ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_MESH>") )
+ if ( ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_MESH>") )
{
read_pseudo_mesh(ifs);
ModuleBase::GlobalFunc::SCAN_END(ifs, "</PP_MESH>");
@@ -1052,7 +1052,7 @@ if (this->nlcc)
+ if (this->nlcc)
{
ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_NLCC>");
read_pseudo_nlcc(ifs);
@@ -1061,12 +1061,12 @@ ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_LOCAL>");
+ ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_LOCAL>");
read_pseudo_local(ifs);
ModuleBase::GlobalFunc::SCAN_END(ifs, "</PP_LOCAL>");
与 类似的还有 , , , 从 则可以读取旋轨耦合相关信息：
-if (has_so)
+ if (has_so)
{
ModuleBase::GlobalFunc::SCAN_BEGIN (ifs,"<PP_ADDINFO>");
read_pseudo_so (ifs);
@@ -1140,7 +1140,7 @@ if(error==0)
+ if(error==0)
{
if(this->atoms[i].flag_empty_element) upf.set_empty_element();
error_ap = upf.average_p(GlobalV::soc_lambda);
@@ -1148,7 +1148,7 @@ if(GlobalV::MY_RANK==0)
+ if(GlobalV::MY_RANK==0)
{
atoms[i].ncpp.set_pseudo_nc( upf );
....
@@ -1178,7 +1178,7 @@ }
No results matching "
var gitbook = gitbook || [];
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diff --git a/_book/develop-path1.html b/_book/develop-path1.html
index 1de92b86..d41c1be3 100644
--- a/_book/develop-path1.html
+++ b/_book/develop-path1.html
@@ -1112,8 +1112,8 @@ <
Input_Conv::Convert()
这个函数实现了从 Input 类对象的数据成员到 GlobalV 和 GlobalC 等全局变量集合的转换。相当于从 Input 到 GlobalV 和 GlobalC，以及其他直接的类的参数上载：
-其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
+其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
void Input_Conv::Convert(void)
{
....
@@ -1308,7 +1308,7 @@
不要忘记我们已经完成 Driver::reading() 函数内容，到达 Driver::atomic_world()。这一点从本文档设置的分级目录中也可以看得到。
-cppvoid Driver::init()
+void Driver::init()
{
this->reading();
this->atomic_world(); // <- here!
@@ -1518,7 +1518,7 @@ 从 SIAB 到 ABACUS（一）：准备工作（施工中 🚧）
下篇：Introduction to ABACUS: Path to PW calculation - Part 2
@@ -1562,7 +1562,7 @@ No results matching "
var gitbook = gitbook || [];
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V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","attributes":{},"skip":false,"key":"1.1.15.5"},{"backlink":"abacus-surface6.html#fig1.1.16.1","level":"1.1.16","list_caption":"Figure: 一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","alt":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","nro":14,"url":"picture/fig_surface6-1.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","attributes":{},"skip":false,"key":"1.1.16.1"},{"backlink":"abacus-surface6.html#fig1.1.16.2","level":"1.1.16","list_caption":"Figure: 静电势（Electrostatic Potential）沿超胞Z轴变化图","alt":"静电势（Electrostatic Potential）沿超胞Z轴变化图","nro":15,"url":"picture/fig_surface6-2.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"静电势（Electrostatic Potential）沿超胞Z轴变化图","attributes":{},"skip":false,"key":"1.1.16.2"},{"backlink":"develop-path4.html#fig1.2.9.1","level":"1.2.9","list_caption":"Figure: ","alt":" 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1)","alt":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","nro":21,"url":"picture/fig_path5-11.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","attributes":{},"skip":false,"key":"1.2.10.3"},{"backlink":"develop-path5.html#fig1.2.10.4","level":"1.2.10","list_caption":"Figure: 1-dimensional example","alt":"1-dimensional example","nro":22,"url":"picture/fig_path5-12.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"1-dimensional example","attributes":{},"skip":false,"key":"1.2.10.4"},{"backlink":"develop-path5.html#fig1.2.10.5","level":"1.2.10","list_caption":"Figure: 2-dimensional example","alt":"2-dimensional example","nro":23,"url":"picture/fig_path5-13.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"2-dimensional example","attributes":{},"skip":false,"key":"1.2.10.5"}]},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"develop-path1.md","mtime":"2023-10-04T14:18:52.079Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-10-04T15:29:41.868Z"},"basePath":".","book":{"language":""}});
});
diff --git a/_book/develop-path2.html b/_book/develop-path2.html
index 191dfe74..d829579b 100644
--- a/_book/develop-path2.html
+++ b/_book/develop-path2.html
@@ -1028,7 +1028,7 @@ // a(i) is lattice vector
}
-我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
+我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
UnitCell::read_atom_positions()
🔧重构思考
@@ -1042,7 +1042,7 @@
::
GlobalFunc::READ_VALUE( ifpos, Coordinate);
STRU 第二行指定坐标类型，被读取为 UnitCell::Coordinate。UnitCell::Coordinate 在 STRU 里有不同选项，⚙ 决定原子的具体位置和单位：
-if(Coordinate != "Cartesian"
+ if(Coordinate != "Cartesian"
&& Coordinate != "Direct"
&& Coordinate != "Cartesian_angstrom"
&& Coordinate != "Cartesian_au"
@@ -1092,7 +1092,7 @@ int na = 0;
+ int na = 0;
this->nat = 0;
assert(ntype>0);
for (int it = 0;it < ntype; it++)
@@ -1105,7 +1105,7 @@ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
bool sequence_match = false;
for(int it2=0; it2<ntype; it2++)
{
@@ -1121,7 +1121,7 @@ }
读取当前原子类型的 starting_magnetization、原子总数 na
-ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
...
ModuleBase::GlobalFunc::READ_VALUE(ifpos, na);
this->atoms[it].na = na;
@@ -1149,17 +1149,17 @@ [
it].m_loc_ = new ModuleBase::Vector3<double>[na];
⚙ 然后在 ATOMIC_POSITIONS 中读取：
-atoms[it].mass = this->atom_mass[it];
+ atoms[it].mass = this->atom_mass[it];
❗ 此处的 atoms[it].mass 与 this->atom_mass[it] 的用法与 atomis[it].label 与 this->atom_label[it] 不同：传值 vs 核对。
接下来读取类中每个原子的速度信息，在做分子动力学模拟的时候可能需要用到：
-for (int ia = 0;ia < na; ia++)
+ for (int ia = 0;ia < na; ia++)
{
ifpos >> v.x >> v.y >> v.z;
然而，当前 STRU 文件在 ATOMIC_POSITIONS 的设计比较复杂，其可以包括任何一组 atom-specific 数据，且数量和顺序均不受限制，这导致判断条件变得复杂，详见 module_cell/read_atoms.cpp:line 536 - 567（link）。
atoms[it].mag 的赋值并非直接读取：
-else if ( tmpid == "mag" || tmpid == "magmom")
+ else if ( tmpid == "mag" || tmpid == "magmom")
{
set_element_mag_zero = true;
double tmpamg=0; ifpos >> tmpamg;
@@ -1185,7 +1185,7 @@ }
⚙ 若 mag/magmom 后有一个值，则读取其值赋给 atoms[it]::mag[ia]，将 input_vec_mag 置为 false，若有三个值，则三个值依次被传入 atoms[it].m_loc_[ia].x, atoms[it].m_loc_[ia].y 和 atoms[it].m_loc_[ia].z，并将 input_vec_mag 置为 true，之后其向量模长为 atoms[it]::mag[ia]，然后在使用 angle1, angle2 来重新生成 mag。
-if(GlobalV::NSPIN==4)
+ if(GlobalV::NSPIN==4)
{
if(GlobalV::NONCOLIN)
{
@@ -1227,7 +1227,7 @@ pw.x input description
ABACUS 对 nspin=4 情况的参数处理：
//module_io/input_conv.cpp line 376
if (INPUT.noncolin || INPUT.lspinorb)
@@ -1312,7 +1312,7 @@
UnitCell::setup_cell(): the rest, and an example of backtracking unclear variable
离开 STRU 文件的解析部分，接下来计算了初始磁化强度：
-//after read STRU, calculate initial total magnetization when NSPIN=2
+ //after read STRU, calculate initial total magnetization when NSPIN=2
if(GlobalV::NSPIN == 2 && !GlobalV::TWO_EFERMI)
{
for(int it = 0;it<this->ntype; it++)
@@ -1326,31 +1326,25 @@ if (std::abs(INPUT.nupdown) > 1e-6)
- {
- GlobalV::TWO_EFERMI = true;
- GlobalV::nupdown = INPUT.nupdown;
- }
-
-因此 GlobalV::TWO_EFERMI 变量实际依赖于 INPUT.nupdown。
-
-- 接下来在
module_io/input.cpp 中寻找含 INPUT.nupdown 的 if(strcmp(...)) 单元，查看在 INPUT 文件中是何参数赋予其具体值：
-
-else if (strcmp("nupdown", word) == 0)
+在 module_io/input_conv.cpp 中寻找该变量，是何变量赋其值，发现： if (std::abs(INPUT.nupdown) > 1e-6)
{
- read_value(ifs, nupdown);
- }
+ GlobalV::TWO_EFERMI = true;
+ GlobalV::nupdown = INPUT.nupdown;
+ }
-即 INPUT.nupdown 在 INPUT 中也为 nupdown。接下来打开 Full keyword list 寻找其解释。
-
+ 因此 GlobalV::TWO_EFERMI 变量实际依赖于 INPUT.nupdown。
+接下来在 module_io/input.cpp 中寻找含 INPUT.nupdown 的 if(strcmp(...)) 单元，查看在 INPUT 文件中是何参数赋予其具体值： else if (strcmp("nupdown", word) == 0)
+ {
+ read_value(ifs, nupdown);
+ }
+
+即 INPUT.nupdown 在 INPUT 中也为 nupdown。接下来打开 Full keyword list 寻找其解释。
得到结果，即 nupdown 为 spin up 和 spin down 电子数量差值：
因此该部分逻辑为：若未使用 nupdown 来指定单电子数量，则对每种原子内每个原子，累加其 mag/magmom，即磁矩模长，赋予 GlobalV::nupdown。❗ 但对于两种方式均赋予，但值不一致的情况未进行处理。
接下来根据在 STRU 中读取的晶胞参数，计算晶胞体积，并计算倒空间矢量（在上篇中已经对 latvec, G, GT, GGT 有所介绍，invGGT 的意义也不言自明）：
-this->omega = std::abs( latvec.Det() ) * this->lat0 * lat0 * lat0 ;
+ this->omega = std::abs( latvec.Det() ) * this->lat0 * lat0 * lat0 ;
this->GT = latvec.Inverse();
this->G = GT.Transpose();
@@ -1442,7 +1436,7 @@ =
static_cast<ModulePW::PW_Basis_Big*>(pw_rho);
对于 ESolver 本身，其指针对象 p_esolver 实际上也有类似操作：
-//Some API to operate E_Solver
+ //Some API to operate E_Solver
void init_esolver(ESolver*& p_esolver)
{
//determine type of esolver based on INPUT information
@@ -1907,7 +1901,7 @@ Introduction to ABACUS: Path to PW calculation - Part 1
下篇：Introduction to ABACUS: Path to PW calculation - Part 3
@@ -1951,7 +1945,7 @@ No results matching "
var gitbook = gitbook || [];
gitbook.push(function() {
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V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","attributes":{},"skip":false,"key":"1.1.15.5"},{"backlink":"abacus-surface6.html#fig1.1.16.1","level":"1.1.16","list_caption":"Figure: 一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","alt":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","nro":14,"url":"picture/fig_surface6-1.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","attributes":{},"skip":false,"key":"1.1.16.1"},{"backlink":"abacus-surface6.html#fig1.1.16.2","level":"1.1.16","list_caption":"Figure: 静电势（Electrostatic Potential）沿超胞Z轴变化图","alt":"静电势（Electrostatic Potential）沿超胞Z轴变化图","nro":15,"url":"picture/fig_surface6-2.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"静电势（Electrostatic Potential）沿超胞Z轴变化图","attributes":{},"skip":false,"key":"1.1.16.2"},{"backlink":"develop-path4.html#fig1.2.9.1","level":"1.2.9","list_caption":"Figure: ","alt":" 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});
diff --git a/_book/develop-path3.html b/_book/develop-path3.html
index b8de33d9..09176394 100644
--- a/_book/develop-path3.html
+++ b/_book/develop-path3.html
@@ -750,11 +750,11 @@ Driver
-Driver::atomic_world()
-Driver::driver_run()
-多层继承：Init() functions in esolver class
-Trigger: ESolver_FP::Init()
+Driver
+Driver::atomic_world()
+Driver::driver_run()
+多层继承：Init() functions in esolver class
+Trigger: ESolver_FP::Init()
承接上篇中已经导入的结构信息，以及了解到构造函数及其伴随的变量初始化和 ABACUS 里应用到的 C++ 多态编程，接下来即将（逐渐）步入 ABACUS 的核心内容。我们暂时跳过位于 source/driver_run.cpp:driver_run() 的：
// 3. For these two types of calculations
// nothing else need to be initialized
@@ -830,14 +830,14 @@ }
同理，ESolver_KS 的数据成员，也被 ESolver_KS_PW 继承。ESolver_FP::Init() 首先调用 UnitCell::read_pseudo() 函数进行赝势文件读取，而将赝势文件读取任务放在 FP 层级下，也暗示对于 ABACUS 的第一性原理方法实现来讲，都需要使用赝势。
-Pseudopotential import: UnitCell::read_pseudo()
+Pseudopotential import: UnitCell::read_pseudo()
void UnitCell::read_pseudo(std::ofstream &ofs)
{
read_cell_pseudopots(GlobalV::global_pseudo_dir, ofs);
在解读赝势文件读取功能之前，首先需要对赝势文件的结构和信息做一定程度的了解。
-# ONCV pseudopotential file
-## Section 0: Norm-conserving conditions, generation of pseudopotential and header of exact UPF file
+ONCV pseudopotential file
+Section 0: Norm-conserving conditions, generation of pseudopotential and header of exact UPF file
赝势的意义不言自明，其中模守恒赝势需满足如下条件：
- （赝势得到的能级和全电子方法求解的能级一样，这里 ps 代表 pseudopotentials）
@@ -852,7 +852,7 @@ V_l(r)=\frac{1}{\phi^\text{ps}_l(r)}[\epsilon^\text{ps}_l-\frac{\hbar^2}{2m}\frac{l(l+1)}{r^2}+\frac{\hbar^2}{2m}\frac{d^2}{dr^2}]\phi^\text{ps}_l(r)，解得。
- 扣除中 Hartree、xc 部分，得到：。
-更多细节见
+更多细节见：www.tcm.phy.cam.ac.uk
<UPF version="2.0.1">
<PP_INFO>
<!-- omitted information here -->
@@ -865,8 +865,8 @@ <!-- -->
从 UPF 文件（注意 UPF 文件也有不同的版本，目前 ABACUS 都支持，若有不支持的，可以提 Github 的 issues 进行讨论）开始，截止到 <PP_HEADER> 之前，提供了赝势文件的作者信息，引用信息以及生成赝势文件所使用的程序和相应输入文件，并附带输入文件参数中的解释。由于此块内容对实际计算并不起作用，因此暂时略过。
-## Section 1:
-<PP_HEADER
+Section 1:
+ <PP_HEADER
generated="Generated using ONCVPSP code by D. R. Hamann" author="Martin Schlipf and Francois Gygi"
date="150105" comment=""
element="Al"
@@ -890,8 +890,8 @@ number_of_proj
="4"/>
<PP_HEADER> 部分尽管已经位于所谓“not human readable”区域，但也并非如此。这部分“标签”（HTML 语境）/block 实际上包含了众多精简过的信息，如元素名称（element）、赝势类型（pseudo_type，模守恒，norm-conserving，NC），相对论效应（relativistic），是否为超软赝势等等信息。当前 Al 理论上其原子序数 13，因此有 13 个电子，但此处 z_valence 参数为 11，即有两个 1s 电子被赝化，只留下 2s, 2p, 3s, 3p 电子共 2+6+2+1 个。对于某些元素，甚至有大核赝势与小核赝势之分，根据赝化电子数量不同进行区分。显而易见地，赝化电子数量越多，则计算量越小，但计算结果的精确程度可能更低。
-## Section 2:
-<PP_MESH>
+Section 2:
+ <PP_MESH>
<PP_R type="real" size=" 602" columns="8">
0.0000 0.0100 0.0200 0.0300 0.0400 0.0500 0.0600 0.0700
<!-- omitted information here -->
@@ -907,8 +907,8 @@ </PP_MESH>
No results matching "
var gitbook = gitbook || [];
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diff --git a/_book/develop-path1.html b/_book/develop-path1.html
index 1de92b86..d41c1be3 100644
--- a/_book/develop-path1.html
+++ b/_book/develop-path1.html
@@ -1112,8 +1112,8 @@ <
Input_Conv::Convert()
这个函数实现了从 Input 类对象的数据成员到 GlobalV 和 GlobalC 等全局变量集合的转换。相当于从 Input 到 GlobalV 和 GlobalC，以及其他直接的类的参数上载：
-其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
+其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
void Input_Conv::Convert(void)
{
....
@@ -1308,7 +1308,7 @@
不要忘记我们已经完成 Driver::reading() 函数内容，到达 Driver::atomic_world()。这一点从本文档设置的分级目录中也可以看得到。
-cppvoid Driver::init()
+void Driver::init()
{
this->reading();
this->atomic_world(); // <- here!
@@ -1518,7 +1518,7 @@ 从 SIAB 到 ABACUS（一）：准备工作（施工中 🚧）
下篇：Introduction to ABACUS: Path to PW calculation - Part 2
@@ -1562,7 +1562,7 @@ No results matching "
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});
diff --git a/_book/develop-path2.html b/_book/develop-path2.html
index 191dfe74..d829579b 100644
--- a/_book/develop-path2.html
+++ b/_book/develop-path2.html
@@ -1028,7 +1028,7 @@ // a(i) is lattice vector
}
-我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
+我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
UnitCell::read_atom_positions()
🔧重构思考
@@ -1042,7 +1042,7 @@
::
GlobalFunc::READ_VALUE( ifpos, Coordinate);
STRU 第二行指定坐标类型，被读取为 UnitCell::Coordinate。UnitCell::Coordinate 在 STRU 里有不同选项，⚙ 决定原子的具体位置和单位：
-if(Coordinate != "Cartesian"
+ if(Coordinate != "Cartesian"
&& Coordinate != "Direct"
&& Coordinate != "Cartesian_angstrom"
&& Coordinate != "Cartesian_au"
@@ -1092,7 +1092,7 @@ int na = 0;
+ int na = 0;
this->nat = 0;
assert(ntype>0);
for (int it = 0;it < ntype; it++)
@@ -1105,7 +1105,7 @@ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
bool sequence_match = false;
for(int it2=0; it2<ntype; it2++)
{
@@ -1121,7 +1121,7 @@ }
读取当前原子类型的 starting_magnetization、原子总数 na
-ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
...
ModuleBase::GlobalFunc::READ_VALUE(ifpos, na);
this->atoms[it].na = na;
@@ -1149,17 +1149,17 @@ [
it].m_loc_ = new ModuleBase::Vector3<double>[na];
⚙ 然后在 ATOMIC_POSITIONS 中读取：
-atoms[it].mass = this->atom_mass[it];
+ atoms[it].mass = this->atom_mass[it];
❗ 此处的 atoms[it].mass 与 this->atom_mass[it] 的用法与 atomis[it].label 与 this->atom_label[it] 不同：传值 vs 核对。
接下来读取类中每个原子的速度信息，在做分子动力学模拟的时候可能需要用到：
-for (int ia = 0;ia < na; ia++)
+ for (int ia = 0;ia < na; ia++)
{
ifpos >> v.x >> v.y >> v.z;
然而，当前 STRU 文件在 ATOMIC_POSITIONS 的设计比较复杂，其可以包括任何一组 atom-specific 数据，且数量和顺序均不受限制，这导致判断条件变得复杂，详见 module_cell/read_atoms.cpp:line 536 - 567（link）。
atoms[it].mag 的赋值并非直接读取：
-else if ( tmpid == "mag" || tmpid == "magmom")
+ else if ( tmpid == "mag" || tmpid == "magmom")
{
set_element_mag_zero = true;
double tmpamg=0; ifpos >> tmpamg;
@@ -1185,7 +1185,7 @@ }
⚙ 若 mag/magmom 后有一个值，则读取其值赋给 atoms[it]::mag[ia]，将 input_vec_mag 置为 false，若有三个值，则三个值依次被传入 atoms[it].m_loc_[ia].x, atoms[it].m_loc_[ia].y 和 atoms[it].m_loc_[ia].z，并将 input_vec_mag 置为 true，之后其向量模长为 atoms[it]::mag[ia]，然后在使用 angle1, angle2 来重新生成 mag。
-if(GlobalV::NSPIN==4)
+ if(GlobalV::NSPIN==4)
{
if(GlobalV::NONCOLIN)
{
@@ -1227,7 +1227,7 @@ pw.x input description
ABACUS 对 nspin=4 情况的参数处理：
//module_io/input_conv.cpp line 376
if (INPUT.noncolin || INPUT.lspinorb)
@@ -1312,7 +1312,7 @@
UnitCell::setup_cell(): the rest, and an example of backtracking unclear variable
离开 STRU 文件的解析部分，接下来计算了初始磁化强度：
-//after read STRU, calculate initial total magnetization when NSPIN=2
+ //after read STRU, calculate initial total magnetization when NSPIN=2
if(GlobalV::NSPIN == 2 && !GlobalV::TWO_EFERMI)
{
for(int it = 0;it<this->ntype; it++)
@@ -1326,31 +1326,25 @@ if (std::abs(INPUT.nupdown) > 1e-6)
- {
- GlobalV::TWO_EFERMI = true;
- GlobalV::nupdown = INPUT.nupdown;
- }
-
-因此 GlobalV::TWO_EFERMI 变量实际依赖于 INPUT.nupdown。
-
-- 接下来在
module_io/input.cpp 中寻找含 INPUT.nupdown 的 if(strcmp(...)) 单元，查看在 INPUT 文件中是何参数赋予其具体值：
-
-else if (strcmp("nupdown", word) == 0)
+在 module_io/input_conv.cpp 中寻找该变量，是何变量赋其值，发现： if (std::abs(INPUT.nupdown) > 1e-6)
{
- read_value(ifs, nupdown);
- }
+ GlobalV::TWO_EFERMI = true;
+ GlobalV::nupdown = INPUT.nupdown;
+ }
-即 INPUT.nupdown 在 INPUT 中也为 nupdown。接下来打开 Full keyword list 寻找其解释。
-
+ 因此 GlobalV::TWO_EFERMI 变量实际依赖于 INPUT.nupdown。
+接下来在 module_io/input.cpp 中寻找含 INPUT.nupdown 的 if(strcmp(...)) 单元，查看在 INPUT 文件中是何参数赋予其具体值： else if (strcmp("nupdown", word) == 0)
+ {
+ read_value(ifs, nupdown);
+ }
+
+即 INPUT.nupdown 在 INPUT 中也为 nupdown。接下来打开 Full keyword list 寻找其解释。
得到结果，即 nupdown 为 spin up 和 spin down 电子数量差值：
因此该部分逻辑为：若未使用 nupdown 来指定单电子数量，则对每种原子内每个原子，累加其 mag/magmom，即磁矩模长，赋予 GlobalV::nupdown。❗ 但对于两种方式均赋予，但值不一致的情况未进行处理。
接下来根据在 STRU 中读取的晶胞参数，计算晶胞体积，并计算倒空间矢量（在上篇中已经对 latvec, G, GT, GGT 有所介绍，invGGT 的意义也不言自明）：
-this->omega = std::abs( latvec.Det() ) * this->lat0 * lat0 * lat0 ;
+ this->omega = std::abs( latvec.Det() ) * this->lat0 * lat0 * lat0 ;
this->GT = latvec.Inverse();
this->G = GT.Transpose();
@@ -1442,7 +1436,7 @@ =
static_cast<ModulePW::PW_Basis_Big*>(pw_rho);
No results matching "
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diff --git a/_book/develop-path1.html b/_book/develop-path1.html
index 1de92b86..d41c1be3 100644
--- a/_book/develop-path1.html
+++ b/_book/develop-path1.html
@@ -1112,8 +1112,8 @@ <
Input_Conv::Convert()
这个函数实现了从 Input 类对象的数据成员到 GlobalV 和 GlobalC 等全局变量集合的转换。相当于从 Input 到 GlobalV 和 GlobalC，以及其他直接的类的参数上载：
-其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
+其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
void Input_Conv::Convert(void)
{
....
@@ -1308,7 +1308,7 @@
不要忘记我们已经完成 Driver::reading() 函数内容，到达 Driver::atomic_world()。这一点从本文档设置的分级目录中也可以看得到。
-cppvoid Driver::init()
+void Driver::init()
{
this->reading();
this->atomic_world(); // <- here!
@@ -1518,7 +1518,7 @@ 从 SIAB 到 ABACUS（一）：准备工作（施工中 🚧）
下篇：Introduction to ABACUS: Path to PW calculation - Part 2
@@ -1562,7 +1562,7 @@ No results matching "
var gitbook = gitbook || [];
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st_bottom2D)","attributes":{},"skip":false,"key":"1.2.9.3"},{"backlink":"develop-path5.html#fig1.2.10.1","level":"1.2.10","list_caption":"Figure: 善用Ctrl+F","alt":"善用Ctrl+F","nro":19,"url":"picture/fig_path5-9.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"善用Ctrl+F","attributes":{},"skip":false,"key":"1.2.10.1"},{"backlink":"develop-path5.html#fig1.2.10.2","level":"1.2.10","list_caption":"Figure: klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","alt":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","nro":20,"url":"picture/fig_path5-10.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","attributes":{},"skip":false,"key":"1.2.10.2"},{"backlink":"develop-path5.html#fig1.2.10.3","level":"1.2.10","list_caption":"Figure: klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 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example","attributes":{},"skip":false,"key":"1.2.10.5"}]},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"develop-path1.md","mtime":"2023-10-04T14:18:52.079Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-10-04T15:29:41.868Z"},"basePath":".","book":{"language":""}});
});
diff --git a/_book/develop-path2.html b/_book/develop-path2.html
index 191dfe74..d829579b 100644
--- a/_book/develop-path2.html
+++ b/_book/develop-path2.html
@@ -1028,7 +1028,7 @@ // a(i) is lattice vector
}
-我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
+我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
UnitCell::read_atom_positions()
🔧重构思考
@@ -1042,7 +1042,7 @@
::
GlobalFunc::READ_VALUE( ifpos, Coordinate);
STRU 第二行指定坐标类型，被读取为 UnitCell::Coordinate。UnitCell::Coordinate 在 STRU 里有不同选项，⚙ 决定原子的具体位置和单位：
-if(Coordinate != "Cartesian"
+ if(Coordinate != "Cartesian"
&& Coordinate != "Direct"
&& Coordinate != "Cartesian_angstrom"
&& Coordinate != "Cartesian_au"
@@ -1092,7 +1092,7 @@ int na = 0;
+ int na = 0;
this->nat = 0;
assert(ntype>0);
for (int it = 0;it < ntype; it++)
@@ -1105,7 +1105,7 @@ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
bool sequence_match = false;
for(int it2=0; it2<ntype; it2++)
{
@@ -1121,7 +1121,7 @@ }
读取当前原子类型的 starting_magnetization、原子总数 na
-ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
...
ModuleBase::GlobalFunc::READ_VALUE(ifpos, na);
this->atoms[it].na = na;
@@ -1149,17 +1149,17 @@ [
it].m_loc_ = new ModuleBase::Vector3<double>[na];
No results matching "
var gitbook = gitbook || [];
gitbook.push(function() {
- gitbook.page.hasChanged({"page":{"title":"ABACUS 的 Github 仓库 Issues 处理流程","level":"1.2.4","depth":2,"next":{"title":"ABACUS 线上文档输入参数撰写规范","level":"1.2.5","depth":2,"path":"develop-input.md","ref":"develop-input.md","articles":[]},"previous":{"title":"ABACUS 注释规范：Doxygen 入门 (c++)","level":"1.2.3","depth":2,"path":"develop-dox.md","ref":"develop-dox.md","articles":[]},"dir":"ltr"},"config":{"plugins":["image-captions","auto-scroll-table","splitter","3-ba","theme-comscore","insert-logo","custom-favicon","intopic-toc","anchors","chapter-fold","expandable-chapters","-lunr","-search","search-plus","prism","-highlight","code","mathjax-pro","hide-element","tbfed-pagefooter","disqus","github-buttons","sharing-plus","-sharing","livereload"],"styles":{"website":"styles/website.css","pdf":"styles/pdf.css","epub":"styles/epub.css","mobi":"styles/mobi.css","ebook":"styles/ebook.css","print":"styles/print.css"},"pluginsConfig":{"tbfed-pagefooter":{"copyright":"Copyright © mcresearch.gitee.io 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diff --git a/_book/develop-path1.html b/_book/develop-path1.html
index 1de92b86..d41c1be3 100644
--- a/_book/develop-path1.html
+++ b/_book/develop-path1.html
@@ -1112,8 +1112,8 @@ <
Input_Conv::Convert()
这个函数实现了从 Input 类对象的数据成员到 GlobalV 和 GlobalC 等全局变量集合的转换。相当于从 Input 到 GlobalV 和 GlobalC，以及其他直接的类的参数上载：
-其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
+其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
void Input_Conv::Convert(void)
{
....
@@ -1308,7 +1308,7 @@
不要忘记我们已经完成 Driver::reading() 函数内容，到达 Driver::atomic_world()。这一点从本文档设置的分级目录中也可以看得到。
-cppvoid Driver::init()
+void Driver::init()
{
this->reading();
this->atomic_world(); // <- here!
@@ -1518,7 +1518,7 @@ 从 SIAB 到 ABACUS（一）：准备工作（施工中 🚧）
下篇：Introduction to ABACUS: Path to PW calculation - Part 2
@@ -1562,7 +1562,7 @@ No results matching "
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example","attributes":{},"skip":false,"key":"1.2.10.5"}]},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"develop-path1.md","mtime":"2023-10-04T14:18:52.079Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-10-04T15:29:41.868Z"},"basePath":".","book":{"language":""}});
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diff --git a/_book/develop-path2.html b/_book/develop-path2.html
index 191dfe74..d829579b 100644
--- a/_book/develop-path2.html
+++ b/_book/develop-path2.html
@@ -1028,7 +1028,7 @@ // a(i) is lattice vector
}
-我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
+我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
UnitCell::read_atom_positions()
🔧重构思考
@@ -1042,7 +1042,7 @@
::
GlobalFunc::READ_VALUE( ifpos, Coordinate);
Input_Conv::Convert()
这个函数实现了从 Input 类对象的数据成员到 GlobalV 和 GlobalC 等全局变量集合的转换。相当于从 Input 到 GlobalV 和 GlobalC，以及其他直接的类的参数上载：
其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
其他内容见 ABACUS 第一版开发手册（02. IO 模块，目前暂为飞书内部文档）：
void Input_Conv::Convert(void)
{
....
@@ -1308,7 +1308,7 @@
不要忘记我们已经完成 Driver::reading() 函数内容，到达 Driver::atomic_world()。这一点从本文档设置的分级目录中也可以看得到。
cppvoid Driver::init()
+void Driver::init()
{
this->reading();
this->atomic_world(); // <- here!
@@ -1518,7 +1518,7 @@ 从 SIAB 到 ABACUS（一）：准备工作（施工中 🚧）
下篇：Introduction to ABACUS: Path to PW calculation - Part 2
@@ -1562,7 +1562,7 @@ No results matching "
var gitbook = gitbook || [];
gitbook.push(function() {
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});
diff --git a/_book/develop-path2.html b/_book/develop-path2.html
index 191dfe74..d829579b 100644
--- a/_book/develop-path2.html
+++ b/_book/develop-path2.html
@@ -1028,7 +1028,7 @@ // a(i) is lattice vector
}
-我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
+我们约定，LATTICE_CONSTANT无量纲，LATTICE_VECTORS有量纲，STRU文件中原子坐标无量纲。
UnitCell::read_atom_positions()
🔧重构思考
@@ -1042,7 +1042,7 @@
::
STRU 第二行指定坐标类型，被读取为 UnitCell::Coordinate。UnitCell::Coordinate 在 STRU 里有不同选项，⚙ 决定原子的具体位置和单位：
if(Coordinate != "Cartesian"
+ if(Coordinate != "Cartesian"
&& Coordinate != "Direct"
&& Coordinate != "Cartesian_angstrom"
&& Coordinate != "Cartesian_au"
@@ -1092,7 +1092,7 @@ int na = 0;
+ int na = 0;
this->nat = 0;
assert(ntype>0);
for (int it = 0;it < ntype; it++)
@@ -1105,7 +1105,7 @@ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, atoms[it].label);
bool sequence_match = false;
for(int it2=0; it2<ntype; it2++)
{
@@ -1121,7 +1121,7 @@ }
ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
+ ModuleBase::GlobalFunc::READ_VALUE(ifpos, magnet.start_magnetization[it] );
...
ModuleBase::GlobalFunc::READ_VALUE(ifpos, na);
this->atoms[it].na = na;
@@ -1149,17 +1149,17 @@ [
⚙ 然后在 ATOMIC_POSITIONS 中读取：
-atoms[it].mass = this->atom_mass[it];
+ atoms[it].mass = this->atom_mass[it];
❗ 此处的 atoms[it].mass 与 this->atom_mass[it] 的用法与 atomis[it].label 与 this->atom_label[it] 不同：传值 vs 核对。
接下来读取类中每个原子的速度信息，在做分子动力学模拟的时候可能需要用到：
-for (int ia = 0;ia < na; ia++)
+ for (int ia = 0;ia < na; ia++)
{
ifpos >> v.x >> v.y >> v.z;
然而，当前 STRU 文件在 ATOMIC_POSITIONS 的设计比较复杂，其可以包括任何一组 atom-specific 数据，且数量和顺序均不受限制，这导致判断条件变得复杂，详见 module_cell/read_atoms.cpp:line 536 - 567（link）。
atoms[it].mag 的赋值并非直接读取：
-else if ( tmpid == "mag" || tmpid == "magmom")
+ else if ( tmpid == "mag" || tmpid == "magmom")
{
set_element_mag_zero = true;
double tmpamg=0; ifpos >> tmpamg;
@@ -1185,7 +1185,7 @@ }
atoms[it]::mag[ia]，将 input_vec_mag 置为 false，若有三个值，则三个值依次被传入 atoms[it].m_loc_[ia].x, atoms[it].m_loc_[ia].y 和 atoms[it].m_loc_[ia].z，并将 input_vec_mag 置为 true，之后其向量模长为 atoms[it]::mag[ia]，然后在使用 angle1, angle2 来重新生成 mag。if(GlobalV::NSPIN==4)
+ if(GlobalV::NSPIN==4)
{
if(GlobalV::NONCOLIN)
{
@@ -1227,7 +1227,7 @@ pw.x input description
ABACUS 对 nspin=4 情况的参数处理：
//module_io/input_conv.cpp line 376
if (INPUT.noncolin || INPUT.lspinorb)
@@ -1312,7 +1312,7 @@
UnitCell::setup_cell(): the rest, and an example of backtracking unclear variable
离开 STRU 文件的解析部分，接下来计算了初始磁化强度：
-//after read STRU, calculate initial total magnetization when NSPIN=2
+ //after read STRU, calculate initial total magnetization when NSPIN=2
if(GlobalV::NSPIN == 2 && !GlobalV::TWO_EFERMI)
{
for(int it = 0;it<this->ntype; it++)
@@ -1326,31 +1326,25 @@ if (std::abs(INPUT.nupdown) > 1e-6)
- {
- GlobalV::TWO_EFERMI = true;
- GlobalV::nupdown = INPUT.nupdown;
- }
-
-因此 GlobalV::TWO_EFERMI 变量实际依赖于 INPUT.nupdown。
-
-- 接下来在
module_io/input.cpp 中寻找含 INPUT.nupdown 的 if(strcmp(...)) 单元，查看在 INPUT 文件中是何参数赋予其具体值：
-
-else if (strcmp("nupdown", word) == 0)
+在 module_io/input_conv.cpp 中寻找该变量，是何变量赋其值，发现： if (std::abs(INPUT.nupdown) > 1e-6)
{
- read_value(ifs, nupdown);
- }
+ GlobalV::TWO_EFERMI = true;
+ GlobalV::nupdown = INPUT.nupdown;
+ }
-即 INPUT.nupdown 在 INPUT 中也为 nupdown。接下来打开 Full keyword list 寻找其解释。
-
+ 因此 GlobalV::TWO_EFERMI 变量实际依赖于 INPUT.nupdown。
+接下来在 module_io/input.cpp 中寻找含 INPUT.nupdown 的 if(strcmp(...)) 单元，查看在 INPUT 文件中是何参数赋予其具体值： else if (strcmp("nupdown", word) == 0)
+ {
+ read_value(ifs, nupdown);
+ }
+
+即 INPUT.nupdown 在 INPUT 中也为 nupdown。接下来打开 Full keyword list 寻找其解释。
得到结果，即 nupdown 为 spin up 和 spin down 电子数量差值：
因此该部分逻辑为：若未使用 nupdown 来指定单电子数量，则对每种原子内每个原子，累加其 mag/magmom，即磁矩模长，赋予 GlobalV::nupdown。❗ 但对于两种方式均赋予，但值不一致的情况未进行处理。
接下来根据在 STRU 中读取的晶胞参数，计算晶胞体积，并计算倒空间矢量（在上篇中已经对 latvec, G, GT, GGT 有所介绍，invGGT 的意义也不言自明）：
-this->omega = std::abs( latvec.Det() ) * this->lat0 * lat0 * lat0 ;
+ this->omega = std::abs( latvec.Det() ) * this->lat0 * lat0 * lat0 ;
this->GT = latvec.Inverse();
this->G = GT.Transpose();
@@ -1442,7 +1436,7 @@ =
对于 ESolver 本身，其指针对象 p_esolver 实际上也有类似操作：
-//Some API to operate E_Solver
+ //Some API to operate E_Solver
void init_esolver(ESolver*& p_esolver)
{
//determine type of esolver based on INPUT information
@@ -1907,7 +1901,7 @@ Introduction to ABACUS: Path to PW calculation - Part 1
下篇：Introduction to ABACUS: Path to PW calculation - Part 3
@@ -1951,7 +1945,7 @@ No results matching "
var gitbook = gitbook || [];
gitbook.push(function() {
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","nro":16,"url":"picture/fig_path4-1.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":" ","attributes":{},"skip":false,"key":"1.2.9.1"},{"backlink":"develop-path4.html#fig1.2.9.2","level":"1.2.9","list_caption":"Figure: PW_Basis::distribute_r()：设一个pool中有5个processors","alt":"PW_Basis::distribute_r()：设一个pool中有5个processors","nro":17,"url":"picture/fig_path4-2.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"PW_Basis::distribute_r()：设一个pool中有5个processors","attributes":{},"skip":false,"key":"1.2.9.2"},{"backlink":"develop-path4.html#fig1.2.9.3","level":"1.2.9","list_caption":"Figure: this->count_pw_st(st_length2D, st_bottom2D)","alt":"this->count_pw_st(st_length2D, st_bottom2D)","nro":18,"url":"picture/fig_path4-3.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"this->count_pw_st(st_length2D, st_bottom2D)","attributes":{},"skip":false,"key":"1.2.9.3"},{"backlink":"develop-path5.html#fig1.2.10.1","level":"1.2.10","list_caption":"Figure: 善用Ctrl+F","alt":"善用Ctrl+F","nro":19,"url":"picture/fig_path5-9.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"善用Ctrl+F","attributes":{},"skip":false,"key":"1.2.10.1"},{"backlink":"develop-path5.html#fig1.2.10.2","level":"1.2.10","list_caption":"Figure: klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","alt":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","nro":20,"url":"picture/fig_path5-10.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","attributes":{},"skip":false,"key":"1.2.10.2"},{"backlink":"develop-path5.html#fig1.2.10.3","level":"1.2.10","list_caption":"Figure: klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","alt":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","nro":21,"url":"picture/fig_path5-11.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","attributes":{},"skip":false,"key":"1.2.10.3"},{"backlink":"develop-path5.html#fig1.2.10.4","level":"1.2.10","list_caption":"Figure: 1-dimensional example","alt":"1-dimensional example","nro":22,"url":"picture/fig_path5-12.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"1-dimensional example","attributes":{},"skip":false,"key":"1.2.10.4"},{"backlink":"develop-path5.html#fig1.2.10.5","level":"1.2.10","list_caption":"Figure: 2-dimensional example","alt":"2-dimensional example","nro":23,"url":"picture/fig_path5-13.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"2-dimensional example","attributes":{},"skip":false,"key":"1.2.10.5"}]},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"develop-path2.md","mtime":"2023-10-04T14:37:12.149Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-10-04T15:29:41.868Z"},"basePath":".","book":{"language":""}});
});
diff --git a/_book/develop-path3.html b/_book/develop-path3.html
index b8de33d9..09176394 100644
--- a/_book/develop-path3.html
+++ b/_book/develop-path3.html
@@ -750,11 +750,11 @@ Driver
-Driver::atomic_world()
-Driver::driver_run()
-多层继承：Init() functions in esolver class
-Trigger: ESolver_FP::Init()
+Driver
+Driver::atomic_world()
+Driver::driver_run()
+多层继承：Init() functions in esolver class
+Trigger: ESolver_FP::Init()
承接上篇中已经导入的结构信息，以及了解到构造函数及其伴随的变量初始化和 ABACUS 里应用到的 C++ 多态编程，接下来即将（逐渐）步入 ABACUS 的核心内容。我们暂时跳过位于 source/driver_run.cpp:driver_run() 的：
// 3. For these two types of calculations
// nothing else need to be initialized
@@ -830,14 +830,14 @@ }
同理，ESolver_KS 的数据成员，也被 ESolver_KS_PW 继承。ESolver_FP::Init() 首先调用 UnitCell::read_pseudo() 函数进行赝势文件读取，而将赝势文件读取任务放在 FP 层级下，也暗示对于 ABACUS 的第一性原理方法实现来讲，都需要使用赝势。
-Pseudopotential import: UnitCell::read_pseudo()
+Pseudopotential import: UnitCell::read_pseudo()
void UnitCell::read_pseudo(std::ofstream &ofs)
{
read_cell_pseudopots(GlobalV::global_pseudo_dir, ofs);
在解读赝势文件读取功能之前，首先需要对赝势文件的结构和信息做一定程度的了解。
-# ONCV pseudopotential file
-## Section 0: Norm-conserving conditions, generation of pseudopotential and header of exact UPF file
+ONCV pseudopotential file
+Section 0: Norm-conserving conditions, generation of pseudopotential and header of exact UPF file
赝势的意义不言自明，其中模守恒赝势需满足如下条件：
- （赝势得到的能级和全电子方法求解的能级一样，这里 ps 代表 pseudopotentials）
@@ -852,7 +852,7 @@ V_l(r)=\frac{1}{\phi^\text{ps}_l(r)}[\epsilon^\text{ps}_l-\frac{\hbar^2}{2m}\frac{l(l+1)}{r^2}+\frac{\hbar^2}{2m}\frac{d^2}{dr^2}]\phi^\text{ps}_l(r)，解得。
- 扣除中 Hartree、xc 部分，得到：。
-更多细节见
+更多细节见：www.tcm.phy.cam.ac.uk
<UPF version="2.0.1">
<PP_INFO>
<!-- omitted information here -->
@@ -865,8 +865,8 @@ <!-- -->
<PP_HEADER> 之前，提供了赝势文件的作者信息，引用信息以及生成赝势文件所使用的程序和相应输入文件，并附带输入文件参数中的解释。由于此块内容对实际计算并不起作用，因此暂时略过。<PP_HEADER
+Section 1:
+ <PP_HEADER
generated="Generated using ONCVPSP code by D. R. Hamann" author="Martin Schlipf and Francois Gygi"
date="150105" comment=""
element="Al"
@@ -890,8 +890,8 @@ number_of_proj
="4"/>
<PP_HEADER> 部分尽管已经位于所谓“not human readable”区域，但也并非如此。这部分“标签”（HTML 语境）/block 实际上包含了众多精简过的信息，如元素名称（element）、赝势类型（pseudo_type，模守恒，norm-conserving，NC），相对论效应（relativistic），是否为超软赝势等等信息。当前 Al 理论上其原子序数 13，因此有 13 个电子，但此处 z_valence 参数为 11，即有两个 1s 电子被赝化，只留下 2s, 2p, 3s, 3p 电子共 2+6+2+1 个。对于某些元素，甚至有大核赝势与小核赝势之分，根据赝化电子数量不同进行区分。显而易见地，赝化电子数量越多，则计算量越小，但计算结果的精确程度可能更低。<PP_MESH>
+Section 2:
+ <PP_MESH>
<PP_R type="real" size=" 602" columns="8">
0.0000 0.0100 0.0200 0.0300 0.0400 0.0500 0.0600 0.0700
<!-- omitted information here -->
@@ -907,8 +907,8 @@ </PP_MESH>
这部分开始出现了关于实空间格点相关量的定义。在 tag 中不仅指定数据类型为实数，也指定当前数据的长度（size），以及数据存储的列数（columns = 8）。PP_R 为格点坐标，PP_RAB 则为格点间距。
## Section 3:
-<PP_LOCAL type="real" size=" 602" columns="4">
+Section 3:
+ <PP_LOCAL type="real" size=" 602" columns="4">
-4.5793174225E+01 -4.5788454271E+01 -4.5774276797E+01 -4.5750659428E+01
<!-- omitted information here -->
-3.6912752197E+00 -3.6850921941E+00 -3.6789298138E+00 -3.6727880140E+00
@@ -917,8 +917,8 @@ <PP_LOCAL>
<PP_R> 和 <PP_RAB> 所描述的实空间格点上。。<PP_LOCAL> 正是赝势的局域势部分。
<PP_NONLOCAL>
+Section 4:
+ <PP_NONLOCAL>
<PP_BETA.1
type="real"
size=" 602"
@@ -938,8 +938,8 @@ cutoff_radius_index
=" 246" cutoff_radius=" 2.4500000000E+00" >
## Section 5: and
+Section 5: and
<PP_PSWFC>
</PP_PSWFC>
<PP_RHOATOM type="real" size=" 602" columns="4">
@@ -975,7 +975,7 @@ |\beta\rangle和 pswfc 已经乘径向坐标。
-# UnitCell::read_cell_pseudopots()
+UnitCell::read_cell_pseudopots()
link to Github -> link
void UnitCell::read_cell_pseudopots(const std::string &pp_dir, std::ofstream &log)
{
@@ -1030,7 +1030,7 @@ while (ifs.good())
+ while (ifs.good())
{
ifs >> dummy;
if(dummy=="<PP_HEADER>")
@@ -1044,7 +1044,7 @@ if ( ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_MESH>") )
+ if ( ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_MESH>") )
{
read_pseudo_mesh(ifs);
ModuleBase::GlobalFunc::SCAN_END(ifs, "</PP_MESH>");
@@ -1052,7 +1052,7 @@ if (this->nlcc)
+ if (this->nlcc)
{
ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_NLCC>");
read_pseudo_nlcc(ifs);
@@ -1061,12 +1061,12 @@ ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_LOCAL>");
+ ModuleBase::GlobalFunc::SCAN_BEGIN(ifs, "<PP_LOCAL>");
read_pseudo_local(ifs);
ModuleBase::GlobalFunc::SCAN_END(ifs, "</PP_LOCAL>");
与 类似的还有 , , , 从 则可以读取旋轨耦合相关信息：
-if (has_so)
+ if (has_so)
{
ModuleBase::GlobalFunc::SCAN_BEGIN (ifs,"<PP_ADDINFO>");
read_pseudo_so (ifs);
@@ -1140,7 +1140,7 @@ if(error==0)
+ if(error==0)
{
if(this->atoms[i].flag_empty_element) upf.set_empty_element();
error_ap = upf.average_p(GlobalV::soc_lambda);
@@ -1148,7 +1148,7 @@ if(GlobalV::MY_RANK==0)
+ if(GlobalV::MY_RANK==0)
{
atoms[i].ncpp.set_pseudo_nc( upf );
....
@@ -1178,7 +1178,7 @@ }
该函数属于类 pseudo_nc，而 pseudo_nc 对象为 atom 的数据成员，atoms 则为 UnitCell 的数据成员。pseudo_nc::set_pseudo_h()，pseudo_nc::set_pseudo_atom 和 pseudo_nc::set_pseudo_vl 的内容在此省略，但其分别为将 Hamilton, 原子性质和 Vlocal 相关数据从 upf 对象拷贝。之后(1)使用 lll 刷新为 upf 对象的 projectors 的角动量，然后计算出磁角动量区分时的 projector 个数。(2)取所有 projector 衰减到 0 时候的最大最普适半径。
# 赝势信息后处理
+赝势信息后处理
回到 module_cell/unitcell.cpp line 663，接下来为每个原子创建目录，在目录中写 [原子label].NONLOCAL 文件。[label].NONLOCAL 文件中内容包含 <HEADER>, <DIJ> 和 <PP_BETA> 三个 tag。
<HEADER> 中包含内容：
ofs << "<HEADER>" << std::endl;
@@ -1222,21 +1222,61 @@ }
# 赝势信息分发：UnitCell::bcast_unitcell2(void)
+赝势信息分发：UnitCell::bcast_unitcell2(void)
#ifdef __MPI#ifdef __MPI
+ bcast_unitcell2();
+#endif
+// module_cell/unitcell.cpp:bcast_unitcell2()
+void UnitCell::bcast_unitcell2(void)
+{
+ for (int i = 0; i < ntype; i++)
+ {
+ atoms[i].bcast_atom2();
+ }
+ return;
+}
+// module_cell/atom_spec.cpp:Atom::bcast_atom2()
+void Atom::bcast_atom2()
+{
+ this->ncpp.bcast_atom_pseudo();
+}
+// module_cell/atom_pseudo.cpp::Atom_pseudo::bcast_atom_pseudo()
+void Atom_pseudo::bcast_atom_pseudo(void)
+{
+....
+ Parallel_Common::bcast_int( lmax );
+....
+ Parallel_Common::bcast_double( etotps );
+....
+ Parallel_Common::bcast_bool( tvanp );
+....
+ Parallel_Common::bcast_string( psd );
+....
+ // below two 'bcast_double' lines of codes seem to have bugs,
+ // on some computers, the code will stuck here for ever.
+ // mohan note 2021-04-28
+ Parallel_Common::bcast_double( dion.c , nbeta * nbeta);
+ Parallel_Common::bcast_double( betar.c, nr * nc );
+}
+#endiffor(int it=0; it<ntype; it++)
+ for(int it=0; it<ntype; it++)
{
if(atoms[0].ncpp.xc_func !=atoms[it].ncpp.xc_func)
{
-# STRU 结构检查：UnitCell::check_structure()
+STRU 结构检查：UnitCell::check_structure()
检验结构中任意两原子之间距离是否大于其固定倍数（<1）的共价半径和，
-check_structure(GlobalV::MIN_DIST_COEF);
+ check_structure(GlobalV::MIN_DIST_COEF);
-# 计算轨道数：UnitCell::cal_natomwfc()
+计算轨道数：UnitCell::cal_natomwfc()
UnitCell::cal_natomwfc() 函数计算所有种类的原子轨道数量加和，对于非 nspin=4，即非 soc（自旋轨道耦合）情况，角量子数 l 和 s 非耦合，l 单独可以作为好的量子数来区分量子态，因此对于每个赝势中定义的 wfc，若其对应 occupation 大于等于 0（即有效 wfc），则对应于其角量子数 l，轨道数量增加 2l+1，即计数其磁量子数 m，也相当于对 alpha 和 beta spin 的单独计数。对于 nspin=4 的情况，若考虑 soc，则轨道数对 j=l+s 的情况，当前原子种类当前角量子数对应轨道数量记为 2l+1+1，否则为 2l+1。对于非 soc 但 nspin=4，当前原子种类轨道当前角量子数对应轨道数量记(2l+1)*2：
void UnitCell::cal_natomwfc(std::ofstream &log)
{
@@ -1291,9 +1331,9 @@ 计算跨原子种类最大角量子数 UnitCell::lmax 和某 l 对应最大 zeta 数 UnitCell::nmax，以及跨原子种类的类内 zeta 数总和最大值 UnitCell::nmax_total
寻找赝势中最大角量子数 UnitCell::lmax_ppwf。
-# 价电子数核对
+价电子数核对
核对赝势中定义的价电子数与 ABACUS 预置库中原子的最小价电子数
-# 获取最大格点数量：UnitCell::cal_meshx()
+获取最大格点数量：UnitCell::cal_meshx()
计算跨原子种类的最大格点数量，存储在 UnitCell::meshx 中，目前 ABACUS 代码中变量命名后缀 x 可能代表 max，正如之前看到 npwx 等。
至此，我们离开函数 UnitCell::read_pseudo()，回到 ModuleESolver::ESolver_FP::Init() 函数。
@@ -1304,7 +1344,7 @@ Introduction to ABACUS: Path to PW calculation - Part 2
下篇：Introduction to ABACUS: Path to PW calculation - Part 4
@@ -1348,7 +1388,7 @@ No results matching "
var gitbook = gitbook || [];
gitbook.push(function() {
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采用PBE交换关联泛函和自旋极化得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出不加电场时，两个自旋方向的能带图几乎一样，都有带隙。","alt":"采用PBE交换关联泛函和自旋极化得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出不加电场时，两个自旋方向的能带图几乎一样，都有带隙。","nro":12,"url":"picture/fig_surface5-4.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"采用PBE交换关联泛函和自旋极化得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出不加电场时，两个自旋方向的能带图几乎一样，都有带隙。","attributes":{},"skip":false,"key":"1.1.15.4"},{"backlink":"abacus-surface5.html#fig1.1.15.5","level":"1.1.15","list_caption":"Figure: 采用PBE交换关联泛函和自旋极化，再给体系加上0.1 V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","alt":"采用PBE交换关联泛函和自旋极化，再给体系加上0.1 V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","nro":13,"url":"picture/fig_surface5-5.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"采用PBE交换关联泛函和自旋极化，再给体系加上0.1 V/Å的电场得到的二维nanoribbon的能带图。蓝色和红色代表自旋极化方向不同时对应的两副能带图像，可以看出加了能带之后，其中一个自旋方向的能带图出现费米面附近的交叠，呈现金属性质，另外一个自旋方向的能带图依旧保持在费米面处的能隙。","attributes":{},"skip":false,"key":"1.1.15.5"},{"backlink":"abacus-surface6.html#fig1.1.16.1","level":"1.1.16","list_caption":"Figure: 一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","alt":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","nro":14,"url":"picture/fig_surface6-1.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"一个水分子位于超胞中，红色代表氧原子，白色代表氢原子","attributes":{},"skip":false,"key":"1.1.16.1"},{"backlink":"abacus-surface6.html#fig1.1.16.2","level":"1.1.16","list_caption":"Figure: 静电势（Electrostatic Potential）沿超胞Z轴变化图","alt":"静电势（Electrostatic Potential）沿超胞Z轴变化图","nro":15,"url":"picture/fig_surface6-2.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"静电势（Electrostatic Potential）沿超胞Z轴变化图","attributes":{},"skip":false,"key":"1.1.16.2"},{"backlink":"develop-path4.html#fig1.2.9.1","level":"1.2.9","list_caption":"Figure: ","alt":" ","nro":16,"url":"picture/fig_path4-1.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":" ","attributes":{},"skip":false,"key":"1.2.9.1"},{"backlink":"develop-path4.html#fig1.2.9.2","level":"1.2.9","list_caption":"Figure: PW_Basis::distribute_r()：设一个pool中有5个processors","alt":"PW_Basis::distribute_r()：设一个pool中有5个processors","nro":17,"url":"picture/fig_path4-2.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"PW_Basis::distribute_r()：设一个pool中有5个processors","attributes":{},"skip":false,"key":"1.2.9.2"},{"backlink":"develop-path4.html#fig1.2.9.3","level":"1.2.9","list_caption":"Figure: this->count_pw_st(st_length2D, st_bottom2D)","alt":"this->count_pw_st(st_length2D, st_bottom2D)","nro":18,"url":"picture/fig_path4-3.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"this->count_pw_st(st_length2D, st_bottom2D)","attributes":{},"skip":false,"key":"1.2.9.3"},{"backlink":"develop-path5.html#fig1.2.10.1","level":"1.2.10","list_caption":"Figure: 善用Ctrl+F","alt":"善用Ctrl+F","nro":19,"url":"picture/fig_path5-9.png","index":1,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"善用Ctrl+F","attributes":{},"skip":false,"key":"1.2.10.1"},{"backlink":"develop-path5.html#fig1.2.10.2","level":"1.2.10","list_caption":"Figure: klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","alt":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","nro":20,"url":"picture/fig_path5-10.png","index":2,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 486: K_Vectors::Monkhorst_Pack_formula(), k_type = 0 and 1","attributes":{},"skip":false,"key":"1.2.10.2"},{"backlink":"develop-path5.html#fig1.2.10.3","level":"1.2.10","list_caption":"Figure: klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","alt":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","nro":21,"url":"picture/fig_path5-11.png","index":3,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"klist.cpp line 520: const int i = mpnx * mpny * (z - 1) + mpnx * (y - 1) + (x - 1)","attributes":{},"skip":false,"key":"1.2.10.3"},{"backlink":"develop-path5.html#fig1.2.10.4","level":"1.2.10","list_caption":"Figure: 1-dimensional example","alt":"1-dimensional example","nro":22,"url":"picture/fig_path5-12.png","index":4,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"1-dimensional example","attributes":{},"skip":false,"key":"1.2.10.4"},{"backlink":"develop-path5.html#fig1.2.10.5","level":"1.2.10","list_caption":"Figure: 2-dimensional example","alt":"2-dimensional example","nro":23,"url":"picture/fig_path5-13.png","index":5,"caption_template":"图 _PAGE_IMAGE_NUMBER_. _CAPTION_","label":"2-dimensional example","attributes":{},"skip":false,"key":"1.2.10.5"}]},"gitbook":"*","description":"国产DFT开源软件ABACUS中文使用教程"},"file":{"path":"develop-path3.md","mtime":"2023-10-04T15:11:45.401Z","type":"markdown"},"gitbook":{"version":"3.2.3","time":"2023-10-04T15:29:41.868Z"},"basePath":".","book":{"language":""}});
});
diff --git a/_book/develop-path4.html b/_book/develop-path4.html
index 1840948c..2b9cddf9 100644
--- a/_book/develop-path4.html
+++ b/_book/develop-path4.html
@@ -750,14 +750,14 @@ Driver
-Driver::atomic_world()
-Driver::driver_run()
-多层继承：Init() functions in esolver class
-Trigger: ESolver_FP::Init()
-平面波格点初始化：PW_Basis:: initgrids()
+Driver
+Driver::atomic_world()
+Driver::driver_run()
+多层继承：Init() functions in esolver class
+Trigger: ESolver_FP::Init()
+平面波格点初始化：PW_Basis:: initgrids()
完成了 INPUT 和 STRU，以及赝势文件的读取环节，接下来我们来到平面波的初始化设置相关部分。
-void ESolver_FP::Init(Input& inp, UnitCell& cell)
+ void ESolver_FP::Init(Input& inp, UnitCell& cell)
{
....
if (inp.nx * inp.ny * inp.nz == 0)
@@ -782,7 +782,7 @@ virtual void initgrids(const double lat0_in,const ModuleBase::Matrix3 latvec_in,
+ virtual void initgrids(const double lat0_in,const ModuleBase::Matrix3 latvec_in,
const double gridecut)
{
// generation of nx, ny and nz are omitted here
@@ -868,7 +868,7 @@ }
❗ 注意：这里还完成了倒空间格点数量 fftnx, fftny 和 fftnz 的赋值。因为 FFT 变换前后的格点数量一般相同，因此 fftnx = nx，fftny = ny，...。
-
+图 1. 然后对平面波在 MPI 进程间进行分发：
//module_esolver/esolver_fp.cpp
void ESolver_FP::Init(Input& inp, UnitCell& cell)
@@ -889,9 +889,9 @@ ::
到这里，我们不得不开始对平面波的 MPI 并行机制有一个大致的认识。在 ABACUS 中，CPU（=processor）首先根据不同的布里渊区 k 点分组被划分成不同的并行池（parallelizaiton pool），每个 pool 都包含几个 k 点，在每个 pool 里面会有完整的对该 k 点求解 Kohn-Sham 方程的过程。因此，在每个 pool 中采用一定数量的 CPU 进程来完成计算。在 INPUT 文件中，KPAR 参数决定了并行池的数量（即 pool 的个数）。换句话说，ABACUS 的 k 点并行机制为，将 k 点（设其数量为 nkpt）分配在 KPAR 个 pool 中，若一共有 nproc 个 processor，则：
- 每个 pool 有
nproc/KPAR个 processor
@@ -899,7 +899,7 @@
## MPI 进程编号：rank
+MPI 进程编号：rank
rank 是一个在 MPI 并行里常被用到的变量。在拥有不止一个 processor 的时候，每个 processor 都具有唯一的编号，称为 rank。如果在每个 processor 都有 rank 的基础上还定义了 pool，以及在每个 pool 中的 processor 数量，则 processor 除了有跨 pool 的全局 rank，也可以有 pool 之内的局部 rank，这部分内容见 module_base/global_variable.cpp:
int NPROC = 1;
int KPAR = 1;
@@ -926,7 +926,7 @@ }
## 并行策略
+并行策略
## OpenMP-MPI 混合编程
+OpenMP-MPI 混合编程
通常来讲，尽管 OpenMP 提供了线程并行，但由于共享内存可能并不存在于 processors 之间，或 computer, nodes 之间，且没有适合的内存共享系统（multi-socket server），此时如果以 OpenMP 放心运行，则可能得出错误结果或直接报错——因为内存无法访问。对于这种情况，需要使用 MPI（Message passing interface）来维持无内存共享处理单元之间的信息交换，以及信息分发和分布计算，而在处理单元内部，即可以共享内存的域内，则可以通过 OpenMP 技术来进行线程级并行。
-# 实空间格点分发
+实空间格点分发
在简单介绍完并行机制后，我们知道，对于未显式以并行方式实现的函数，其运行将在每一个 processor。在接下来的平面波分发过程中，请始终牢记这一理念，尤其在 processor-local 变量和 processor-global 变量的传值过程中。
稍加回溯：
void ESolver_FP::Init(Input& inp, UnitCell& cell)
@@ -968,7 +968,7 @@ ## 实空间：PW_Basis::distribute_r()
+实空间：PW_Basis::distribute_r()
❗Attention
注意，此时实际调用的也是 PW_Basis_Big 而非 PW_Basis 的 distribute_r() 函数。
@@ -1011,8 +1011,8 @@ {
该判断不会 always true。因此 PW_Basis::distribute_r() 将 3D 实空间格点，按照 z 方向进行分发，分给了不同的 processors，并赋值 this->npz，this->nplane, this->startz_current 和 this->nrxx，意义分别为当前 processor 的 z 方向格点数量、xy 平面数量、z 格点的起始索引以及当前 processor 所分得实空间格点总数（分配后 z 方向格点 ×xy 平面格点）。
## 倒空间：PW_Basis::distribute_g()
+倒空间：PW_Basis::distribute_g()
倒空间格点的分发采用了和实空间不同的方式，这主要是因为倒空间“球”的存在（ecutwfc 和 ecutrho），使得非空间中所有点都需要考虑在内，而实空间则并非如此。更一般而言，有限的实空间带来无限的倒空间（即实空间 delta 函数需要无限数量的平面波展开）延展，而有限的倒空间（倒空间 delta 点）带来无限的实空间延展（如一个平面波）。
[] st_bottom2D; delete[] st_length2D; } -🔧重构信息 @@ -1066,7 +1066,7 @@
delete
### 分发最小单元：“棍子” - 准备工作
+分发最小单元：“棍子” - 准备工作
PW_Basis::count_pw_st() 函数（Link）计算了每个(x,y)对应的“棍子”的底部和“长度”，即对倒空间只分辨(x,y)，则会得到沿 z 方向的点的集合，被称为“棍子”。而“棍子”区域内部每一个点都代表一个平面波。“棍子”的底部对应于最小的 iz 值，“根子”的长度则为当前(x,y)所包含的平面波数量：for (int ix = ix_start; ix <= ix_end; ++ix)
@@ -1098,7 +1098,7 @@ }
在倒空间分发平面波时，由于 x/y/z 均等在正负半轴 span，因此常常会涉及到 C++ 不支持负数索引的问题（btw: Python 和 FORTRAN 支持负数索引，但支持方式不同），ABACUS 当前所采取的策略是：
if (x<0) x += this->nx; if (y<0) y += this->ny; if (z<0) z += this->nz;
### “棍子”的分发和分发记录
+“棍子”的分发和分发记录
PW_Basis::collect_st() 和 PW_Basis::divide_sticks_1() 分别排序与分发“棍子”到不同 processor：
- 按照棍子从长到短顺序进行排序，即
st_length2D由大到小排序，然后适用于st_bottom2D等变量
@@ -1136,7 +1136,7 @@
this
### 映射表：OOP？
+映射表：OOP？
this->fftixy2ip, this->istot2ixy, this->ig2isz 和 this->is2fftixy，其意义分别为：
