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‎docs/quick_start/output.md‎

Lines changed: 7 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,13 @@ The following files are the central output files for ABACUS. After executing the
66

77
Different from `INPUT` given by the users, `OUT.suffix/INPUT` contains all parameters in ABACUS.
88

9-
> **Note:** `OUT.suffix/INPUT` contain the initial default of ABACUS instead of the real parameters used in calculations. This file is stored for reproduction in case the default value is changed during development. If you want to figure out the real parameters used in calculations, you can open `OUT.suffix/runing_scf.log` and research corresponding parameter you are interested.
9+
> **Note:** `OUT.suffix/INPUT` contains the **actual parameters used in the calculation**, including:
10+
> 1. **User-specified parameters** (explicitly defined in your input file or command-line arguments, overriding default parameters).
11+
> 2. **System default parameters** (automatically applied when not explicitly provided by the user).
12+
13+
14+
This file ensures calculations can be fully reproduced, even if default values change in future ABACUS versions.
15+
Also notice that in rare cases, a small number of parameters may be dynamically reset to appropriate values during runtime.
1016

1117
For a complete list of input parameters, please consult this [instruction](../advanced/input_files/input-main.md).
1218

‎source/module_base/global_function.cpp‎

Lines changed: 50 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -104,7 +104,11 @@ void DONE(std::ofstream &ofs, const std::string &description, const bool only_ra
104104
return;
105105
}
106106

107-
bool SCAN_BEGIN(std::ifstream &ifs, const std::string &TargetName, const bool restart, const bool ifwarn)
107+
108+
bool SCAN_BEGIN(std::ifstream &ifs,
109+
const std::string &TargetName,
110+
const bool restart,
111+
const bool ifwarn)
108112
{
109113
std::string SearchName;
110114
bool find = false;
@@ -130,6 +134,51 @@ bool SCAN_BEGIN(std::ifstream &ifs, const std::string &TargetName, const bool re
130134
return find;
131135
}
132136

137+
138+
bool SCAN_LINE_BEGIN(std::ifstream &ifs,
139+
const std::string &TargetName,
140+
const bool restart,
141+
const bool ifwarn)
142+
{
143+
bool find = false;
144+
if (restart)
145+
{
146+
ifs.clear();
147+
ifs.seekg(0);
148+
}
149+
ifs.rdstate();
150+
151+
std::string line;
152+
while (std::getline(ifs,line))
153+
{
154+
//! obtain the first character, should not be #
155+
size_t first_char_pos = line.find_first_not_of(" \t");
156+
if (first_char_pos != std::string::npos && line[first_char_pos] == '#')
157+
{
158+
continue;
159+
}
160+
161+
//! search in each line
162+
std::istringstream iss(line);
163+
std::string SearchName;
164+
while (iss >> SearchName)
165+
{
166+
if (SearchName == TargetName)
167+
{
168+
find = true;
169+
//std::cout << " search name = " << SearchName << std::endl;
170+
return find;
171+
}
172+
}
173+
}
174+
175+
if (!find && ifwarn)
176+
{
177+
GlobalV::ofs_warning << " In SCAN_LINE_BEGIN, can't find: " << TargetName << " block." << std::endl;
178+
}
179+
return find;
180+
}
181+
133182
void SCAN_END(std::ifstream &ifs, const std::string &TargetName, const bool ifwarn)
134183
{
135184
std::string SearchName;

‎source/module_base/global_function.h‎

Lines changed: 20 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
1-
#ifndef W_ABACUS_DEVELOP_ABACUS_DEVELOP_SOURCE_MODULE_BASE_GLOBAL_FUNCTION_H
2-
#define W_ABACUS_DEVELOP_ABACUS_DEVELOP_SOURCE_MODULE_BASE_GLOBAL_FUNCTION_H
1+
#ifndef GLOBAL_FUNCTION_H
2+
#define GLOBAL_FUNCTION_H
33

44
#include "blas_connector.h"
55
#include "global_function-func_each_2.h" // Peize Lin add 2016-09-07
@@ -145,13 +145,26 @@ static void READ_VALUE(std::ifstream& ifs, T& v)
145145
return;
146146
}
147147

148-
bool SCAN_BEGIN(std::ifstream& ifs, const std::string& TargetName, const bool restart = true, const bool ifwarn = true);
149-
// ifwarn: whether to call GlobalV::ofs_warning when the TargetName is not found, used to avoid invalid warning.
150-
// Mohan warning : the last term can't be written as const bool &restart,
151-
// I don't know why.
148+
//-------------------------------------------------------------
149+
//! The `SCAN_BEGIN` function efficiently searches
150+
//! text files for specified keywords
151+
//-------------------------------------------------------------
152+
bool SCAN_BEGIN(std::ifstream& ifs,
153+
const std::string& TargetName,
154+
const bool restart = true,
155+
const bool ifwarn = true);
156+
157+
//-------------------------------------------------------------
158+
// The `SCAN_LINE_BEGIN` function efficiently searches
159+
// text files for specified keywords while ignoring comment
160+
// lines and whitespace. It skips any line starting with '#'
161+
//-------------------------------------------------------------
162+
bool SCAN_LINE_BEGIN(std::ifstream& ifs,
163+
const std::string& TargetName,
164+
const bool restart = true,
165+
const bool ifwarn = true);
152166

153167
void SCAN_END(std::ifstream& ifs, const std::string& TargetName, const bool ifwarn = true);
154-
// ifwarn: whether to call GlobalV::ofs_warning when the TargetName is not found, used to avoid invalid warning.
155168

156169
template <class T>
157170
static inline void DCOPY(const T& a, T& b, const int& dim)

‎source/module_base/kernels/math_ylm_op.h‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -20,7 +20,7 @@ struct cal_ylm_real_op {
2020
/// @param PI_HALF - ModuleBase::PI_HALF
2121
/// @param FOUR_PI - ModuleBase::FOUR_PI,
2222
/// @param SQRT_INVERSE_FOUR_PI - ModuleBase::SQRT_INVERSE_FOUR_PI,
23-
/// @param g - input array with size npw * 3, GlobalC::wf.get_1qvec_cartesian
23+
/// @param g - input array with size npw * 3, wf.get_1qvec_cartesian
2424
/// @param p - intermediate array
2525
///
2626
/// Output Parameters

‎source/module_basis/module_nao/two_center_bundle.h‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -28,7 +28,7 @@ class TwoCenterBundle
2828
void tabulate(const double lcao_ecut, const double lcao_dk, const double lcao_dr, const double lcao_rmax);
2929

3030
/**
31-
* @brief Overwrites the content of a LCAO_Orbitals object (e.g. GlobalC::ORB)
31+
* @brief Overwrites the content of a LCAO_Orbitals object (e.g. ORB)
3232
* with the current object.
3333
*
3434
* This function provides an interface to the corresponding object in the old module_ao.

‎source/module_cell/read_atom_species.cpp‎

Lines changed: 37 additions & 29 deletions
Original file line numberDiff line numberDiff line change
@@ -13,15 +13,15 @@ bool read_atom_species(std::ifstream& ifa,
1313
UnitCell& ucell)
1414
{
1515
ModuleBase::TITLE("UnitCell","read_atom_species");
16+
1617
const int ntype = ucell.ntype;
1718
std::string word;
1819

1920
//==========================================
2021
// read in information of each type of atom
2122
//==========================================
22-
if( ModuleBase::GlobalFunc::SCAN_BEGIN(ifa, "ATOMIC_SPECIES") )
23+
if( ModuleBase::GlobalFunc::SCAN_LINE_BEGIN(ifa, "ATOMIC_SPECIES") )
2324
{
24-
ifa.ignore(300, '\n');
2525
ModuleBase::GlobalFunc::OUT(ofs_running,"ntype",ntype);
2626
for (int i = 0;i < ntype;i++)
2727
{
@@ -51,7 +51,8 @@ bool read_atom_species(std::ifstream& ifa,
5151

5252
if (!end && ss >> one_string && one_string[0] != '#')
5353
{
54-
if (one_string == "auto" || one_string == "upf" || one_string == "vwr" || one_string == "upf201" || one_string == "blps")
54+
if (one_string == "auto" || one_string == "upf"
55+
|| one_string == "vwr" || one_string == "upf201" || one_string == "blps")
5556
{
5657
ucell.pseudo_type[i] = one_string;
5758
}
@@ -61,15 +62,17 @@ bool read_atom_species(std::ifstream& ifa,
6162
}
6263
else
6364
{
64-
GlobalV::ofs_warning << "unrecongnized pseudopotential type: " << one_string << ", check your STRU file." << std::endl;
65+
GlobalV::ofs_warning << "unrecongnized pseudopotential type: "
66+
<< one_string << ", check your STRU file." << std::endl;
6567
ModuleBase::WARNING_QUIT("read_atom_species", "unrecongnized pseudo type.");
6668
}
6769
}
6870

6971
// Peize Lin test for bsse 2021.04.07
7072
const std::string bsse_label = "empty";
7173
ucell.atoms[i].flag_empty_element =
72-
(search( ucell.atom_label[i].begin(), ucell.atom_label[i].end(), bsse_label.begin(), bsse_label.end() ) != ucell.atom_label[i].end())
74+
(search( ucell.atom_label[i].begin(), ucell.atom_label[i].end(),
75+
bsse_label.begin(), bsse_label.end() ) != ucell.atom_label[i].end())
7376
? true : false;
7477
}
7578
}
@@ -80,7 +83,7 @@ bool read_atom_species(std::ifstream& ifa,
8083
||((PARAM.inp.basis_type == "pw")&&(PARAM.inp.init_wfc.substr(0, 3) == "nao"))
8184
|| PARAM.inp.onsite_radius > 0.0)
8285
{
83-
if( ModuleBase::GlobalFunc::SCAN_BEGIN(ifa, "NUMERICAL_ORBITAL") )
86+
if( ModuleBase::GlobalFunc::SCAN_LINE_BEGIN(ifa, "NUMERICAL_ORBITAL") )
8487
{
8588
for(int i=0; i<ntype; i++)
8689
{
@@ -90,7 +93,7 @@ bool read_atom_species(std::ifstream& ifa,
9093
// caoyu add 2021-03-16
9194
if(PARAM.globalv.deepks_setorb)
9295
{
93-
if (ModuleBase::GlobalFunc::SCAN_BEGIN(ifa, "NUMERICAL_DESCRIPTOR")) {
96+
if (ModuleBase::GlobalFunc::SCAN_LINE_BEGIN(ifa, "NUMERICAL_DESCRIPTOR")) {
9497
ifa >> ucell.descriptor_file;
9598
}
9699
}
@@ -105,7 +108,7 @@ bool read_atom_species(std::ifstream& ifa,
105108
#ifdef __EXX
106109
if( GlobalC::exx_info.info_global.cal_exx || PARAM.inp.rpa )
107110
{
108-
if( ModuleBase::GlobalFunc::SCAN_BEGIN(ifa, "ABFS_ORBITAL") )
111+
if( ModuleBase::GlobalFunc::SCAN_LINE_BEGIN(ifa, "ABFS_ORBITAL") )
109112
{
110113
for(int i=0; i<ntype; i++)
111114
{
@@ -133,7 +136,7 @@ bool read_lattice_constant(std::ifstream& ifa,
133136
double& lat0_angstrom =lat.lat0_angstrom;
134137
std::string& latName = lat.latName;
135138
ModuleBase::Matrix3& latvec = lat.latvec;
136-
if( ModuleBase::GlobalFunc::SCAN_BEGIN(ifa, "LATTICE_CONSTANT") )
139+
if( ModuleBase::GlobalFunc::SCAN_LINE_BEGIN(ifa, "LATTICE_CONSTANT") )
137140
{
138141
ModuleBase::GlobalFunc::READ_VALUE(ifa, lat0);
139142
if(lat0<=0.0)
@@ -153,18 +156,23 @@ bool read_lattice_constant(std::ifstream& ifa,
153156

154157
if(latName=="none")
155158
{
156-
if (ModuleBase::GlobalFunc::SCAN_BEGIN(ifa,
159+
// check the existence of keyword "LATTICE_PARAMETERS"
160+
if (ModuleBase::GlobalFunc::SCAN_LINE_BEGIN(ifa,
157161
"LATTICE_PARAMETERS",
158162
true,
159163
false))
160164
{
161-
ModuleBase::WARNING_QUIT("unitcell::read_lattice_constant","do not use LATTICE_PARAMETERS without explicit specification of lattice type");
165+
ModuleBase::WARNING_QUIT("unitcell::read_lattice_constant",
166+
"do not use LATTICE_PARAMETERS without explicit specification of lattice type");
162167
}
163-
if( !ModuleBase::GlobalFunc::SCAN_BEGIN(ifa, "LATTICE_VECTORS") )
168+
169+
// check the existence of keyword "LATTICE_VECTORS"
170+
if( !ModuleBase::GlobalFunc::SCAN_LINE_BEGIN(ifa, "LATTICE_VECTORS") )
164171
{
165-
ModuleBase::WARNING_QUIT("unitcell::read_lattice_constant","Please set LATTICE_VECTORS in STRU file");
172+
ModuleBase::WARNING_QUIT("unitcell::read_lattice_constant",
173+
"Please set LATTICE_VECTORS in STRU file");
166174
}
167-
else if( ModuleBase::GlobalFunc::SCAN_BEGIN(ifa, "LATTICE_VECTORS") )
175+
else if( ModuleBase::GlobalFunc::SCAN_LINE_BEGIN(ifa, "LATTICE_VECTORS") )
168176
{
169177
// Reading lattice vectors. notice
170178
// here that only one cpu read these
@@ -179,12 +187,13 @@ bool read_lattice_constant(std::ifstream& ifa,
179187
}//supply lattice vectors
180188
else
181189
{
182-
if (ModuleBase::GlobalFunc::SCAN_BEGIN(ifa,
190+
if (ModuleBase::GlobalFunc::SCAN_LINE_BEGIN(ifa,
183191
"LATTICE_VECTORS",
184192
true,
185193
false))
186194
{
187-
ModuleBase::WARNING_QUIT("unitcell::read_lattice_constant","do not use LATTICE_VECTORS along with explicit specification of lattice type");
195+
ModuleBase::WARNING_QUIT("unitcell::read_lattice_constant",
196+
"do not use LATTICE_VECTORS along with explicit specification of lattice type");
188197
}
189198
if(latName=="sc")
190199
{//simple-cubic, ibrav = 1
@@ -210,7 +219,7 @@ bool read_lattice_constant(std::ifstream& ifa,
210219
latvec.e11 = 1.0; latvec.e12 = 0.0; latvec.e13 = 0.0;
211220
latvec.e21 =-0.5; latvec.e22 = e22; latvec.e23 = 0.0;
212221
latvec.e31 = 0.0; latvec.e32 = 0.0; latvec.e33 = 0.0;
213-
if( ModuleBase::GlobalFunc::SCAN_BEGIN(ifa, "LATTICE_PARAMETERS") )
222+
if( ModuleBase::GlobalFunc::SCAN_LINE_BEGIN(ifa, "LATTICE_PARAMETERS") )
214223
{
215224
ModuleBase::GlobalFunc::READ_VALUE(ifa, latvec.e33);
216225
}
@@ -219,7 +228,7 @@ bool read_lattice_constant(std::ifstream& ifa,
219228
{//trigonal, ibrav = 5
220229
double t1 = 0.0;
221230
double t2 = 0.0;
222-
if( ModuleBase::GlobalFunc::SCAN_BEGIN(ifa, "LATTICE_PARAMETERS") )
231+
if( ModuleBase::GlobalFunc::SCAN_LINE_BEGIN(ifa, "LATTICE_PARAMETERS") )
223232
{
224233
double cosab=0.0;
225234
ModuleBase::GlobalFunc::READ_VALUE(ifa, cosab);
@@ -239,15 +248,15 @@ bool read_lattice_constant(std::ifstream& ifa,
239248
latvec.e11 = 1.0; latvec.e12 = 0.0; latvec.e13 = 0.0;
240249
latvec.e21 = 0.0; latvec.e22 = 1.0; latvec.e23 = 0.0;
241250
latvec.e31 = 0.0; latvec.e32 = 0.0; latvec.e33 = 0.0;
242-
if( ModuleBase::GlobalFunc::SCAN_BEGIN(ifa, "LATTICE_PARAMETERS") )
251+
if( ModuleBase::GlobalFunc::SCAN_LINE_BEGIN(ifa, "LATTICE_PARAMETERS") )
243252
{
244253
ModuleBase::GlobalFunc::READ_VALUE(ifa, latvec.e33);
245254
}
246255
}
247256
else if(latName=="bct")
248257
{//body-centered tetragonal, ibrav = 7
249258
double cba = 0.0;
250-
if( ModuleBase::GlobalFunc::SCAN_BEGIN(ifa, "LATTICE_PARAMETERS") )
259+
if( ModuleBase::GlobalFunc::SCAN_LINE_BEGIN(ifa, "LATTICE_PARAMETERS") )
251260
{
252261
ModuleBase::GlobalFunc::READ_VALUE(ifa, cba);
253262
cba = cba / 2.0;
@@ -261,7 +270,7 @@ bool read_lattice_constant(std::ifstream& ifa,
261270
latvec.e11 = 1.0; latvec.e12 = 0.0; latvec.e13 = 0.0;
262271
latvec.e21 = 0.0; latvec.e22 = 0.0; latvec.e23 = 0.0;
263272
latvec.e31 = 0.0; latvec.e32 = 0.0; latvec.e33 = 0.0;
264-
if( ModuleBase::GlobalFunc::SCAN_BEGIN(ifa, "LATTICE_PARAMETERS") )
273+
if( ModuleBase::GlobalFunc::SCAN_LINE_BEGIN(ifa, "LATTICE_PARAMETERS") )
265274
{
266275
ifa >> latvec.e22;
267276
ModuleBase::GlobalFunc::READ_VALUE(ifa, latvec.e33);
@@ -272,7 +281,7 @@ bool read_lattice_constant(std::ifstream& ifa,
272281
latvec.e11 = 0.5; latvec.e12 = 0.0; latvec.e13 = 0.0;
273282
latvec.e21 =-0.5; latvec.e22 = 0.0; latvec.e23 = 0.0;
274283
latvec.e31 = 0.0; latvec.e32 = 0.0; latvec.e33 = 0.0;
275-
if( ModuleBase::GlobalFunc::SCAN_BEGIN(ifa, "LATTICE_PARAMETERS") )
284+
if( ModuleBase::GlobalFunc::SCAN_LINE_BEGIN(ifa, "LATTICE_PARAMETERS") )
276285
{
277286
ifa >> latvec.e12;
278287
latvec.e12 = latvec.e12 / 2.0;
@@ -283,7 +292,7 @@ bool read_lattice_constant(std::ifstream& ifa,
283292
else if(latName=="fco")
284293
{//face-centered orthorhombic, ibrav = 10
285294
double bba = 0.0; double cba = 0.0;
286-
if( ModuleBase::GlobalFunc::SCAN_BEGIN(ifa, "LATTICE_PARAMETERS") )
295+
if( ModuleBase::GlobalFunc::SCAN_LINE_BEGIN(ifa, "LATTICE_PARAMETERS") )
287296
{
288297
ifa >> bba;
289298
ModuleBase::GlobalFunc::READ_VALUE(ifa, cba);
@@ -296,7 +305,7 @@ bool read_lattice_constant(std::ifstream& ifa,
296305
else if(latName=="bco")
297306
{//body-centered orthorhombic, ibrav = 11
298307
double bba = 0.0; double cba = 0.0;
299-
if( ModuleBase::GlobalFunc::SCAN_BEGIN(ifa, "LATTICE_PARAMETERS") )
308+
if( ModuleBase::GlobalFunc::SCAN_LINE_BEGIN(ifa, "LATTICE_PARAMETERS") )
300309
{
301310
ifa >> bba;
302311
ModuleBase::GlobalFunc::READ_VALUE(ifa, cba);
@@ -311,7 +320,7 @@ bool read_lattice_constant(std::ifstream& ifa,
311320
double bba = 0.0; double cba = 0.0;
312321
double cosab = 0.0;
313322
double e21 = 0.0; double e22 = 0.0;
314-
if( ModuleBase::GlobalFunc::SCAN_BEGIN(ifa, "LATTICE_PARAMETERS") )
323+
if( ModuleBase::GlobalFunc::SCAN_LINE_BEGIN(ifa, "LATTICE_PARAMETERS") )
315324
{
316325
ifa >> bba >> cba;
317326
ModuleBase::GlobalFunc::READ_VALUE(ifa, cosab);
@@ -327,7 +336,7 @@ bool read_lattice_constant(std::ifstream& ifa,
327336
double bba = 0.0; double cba = 0.0;
328337
double cosab = 0.0;
329338
double e21 = 0.0; double e22 = 0.0;
330-
if( ModuleBase::GlobalFunc::SCAN_BEGIN(ifa, "LATTICE_PARAMETERS") )
339+
if( ModuleBase::GlobalFunc::SCAN_LINE_BEGIN(ifa, "LATTICE_PARAMETERS") )
331340
{
332341
ifa >> bba >> cba;
333342
ModuleBase::GlobalFunc::READ_VALUE(ifa, cosab);
@@ -348,7 +357,7 @@ bool read_lattice_constant(std::ifstream& ifa,
348357
double cosbc = 0.0;
349358
double sinab = 0.0;
350359
double term = 0.0;
351-
if( ModuleBase::GlobalFunc::SCAN_BEGIN(ifa, "LATTICE_PARAMETERS") )
360+
if( ModuleBase::GlobalFunc::SCAN_LINE_BEGIN(ifa, "LATTICE_PARAMETERS") )
352361
{
353362
ifa >> bba >> cba >> cosab >> cosac;
354363
ModuleBase::GlobalFunc::READ_VALUE(ifa, cosbc);
@@ -363,7 +372,6 @@ bool read_lattice_constant(std::ifstream& ifa,
363372
}
364373
else
365374
{
366-
std::cout << "latname is : " << latName << std::endl;
367375
ModuleBase::WARNING_QUIT("unitcell::read_lattice_constant","latname not supported!");
368376
}
369377
}
@@ -383,4 +391,4 @@ bool read_lattice_constant(std::ifstream& ifa,
383391
return true;
384392
}
385393

386-
}
394+
}

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