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Merge branch 'pod' into pod-updates

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This commit is contained in:
Axel Kohlmeyer
2022-11-28 11:40:40 -05:00
parent ccc24b68ac e78ee616c3
commit ebdce82009
6 changed files with 394 additions and 766 deletions
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52
src/ML-POD/fitpod_command.cpp
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@ -165,16 +165,16 @@ void CFITPOD::read_data_file(double *fitting_weights, std::string &file_format,
char line[MAXLINE],*ptr;
int eof = 0;
while (true) {
//if (comm->me == 0) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fpdata);
if (ptr == nullptr) {
eof = 1;
fclose(fpdata);
}
//}
//MPI_Bcast(&eof,1,MPI_INT,0,world);
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
//MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world);
MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world);
// words = ptrs to all words in line
// strip single and double quotes from words
@ -202,8 +202,8 @@ void CFITPOD::read_data_file(double *fitting_weights, std::string &file_format,
if (keywd == "error_analysis_for_test_data_set") fitting_weights[4] = utils::numeric(FLERR,words[1],false,lmp);
if (keywd == "energy_force_calculation_for_training_data_set") fitting_weights[5] = utils::numeric(FLERR,words[1],false,lmp);
if (keywd == "energy_force_calculation_for_test_data_set") fitting_weights[6] = utils::numeric(FLERR,words[1],false,lmp);
if (keywd == "percentage_training_data_set") fitting_weights[7] = utils::numeric(FLERR,words[1],false,lmp);
if (keywd == "percentage_test_data_set") fitting_weights[8] = utils::numeric(FLERR,words[1],false,lmp);
if (keywd == "fraction_training_data_set") fitting_weights[7] = utils::numeric(FLERR,words[1],false,lmp);
if (keywd == "fraction_test_data_set") fitting_weights[8] = utils::numeric(FLERR,words[1],false,lmp);
if (keywd == "randomize_training_data_set") fitting_weights[9] = utils::numeric(FLERR,words[1],false,lmp);
if (keywd == "randomize_test_data_set") fitting_weights[10] = utils::numeric(FLERR,words[1],false,lmp);
@ -221,8 +221,8 @@ void CFITPOD::read_data_file(double *fitting_weights, std::string &file_format,
utils::logmesg(lmp, "file extension: {}\n", file_extension);
utils::logmesg(lmp, "path to training data set: {}\n", training_path);
utils::logmesg(lmp, "path to test data set: {}\n", test_path);
utils::logmesg(lmp, "training percentage: {}\n", fitting_weights[7]);
utils::logmesg(lmp, "test percentage: {}\n", fitting_weights[8]);
utils::logmesg(lmp, "training fraction: {}\n", fitting_weights[7]);
utils::logmesg(lmp, "test fraction: {}\n", fitting_weights[8]);
utils::logmesg(lmp, "randomize training data set: {}\n", fitting_weights[9]);
utils::logmesg(lmp, "randomize test data set: {}\n", fitting_weights[10]);
utils::logmesg(lmp, "error analysis for training data set: {}\n", fitting_weights[3]);
@ -260,16 +260,16 @@ int CFITPOD::get_number_atom_exyz(std::vector<int>& num_atom, int& num_atom_sum,
// loop over all lines of this xyz file and extract number of atoms and number of configs
while (true) {
//if (comm->me == 0) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == nullptr) {
eof = 1;
fclose(fp);
}
//}
//MPI_Bcast(&eof,1,MPI_INT,0,world);
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
//MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world);
MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world);
// words = ptrs to all words in line
// strip single and double quotes from words
@ -335,16 +335,16 @@ void CFITPOD::read_exyz_file(double *lattice, double *stress, double *energy, do
// loop over all lines of this xyz file and extract training data
while (true) {
//if (comm->me == 0) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == nullptr) {
eof = 1;
fclose(fp);
}
//}
//MPI_Bcast(&eof,1,MPI_INT,0,world);
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
//MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world);
MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world);
// words = ptrs to all words in line
// strip single and double quotes from words
@ -588,11 +588,11 @@ std::vector<int> CFITPOD::shuffle(int start_in, int end_in, int num_in)
return shuffle_vec;
}
std::vector<int> CFITPOD::select(int n, double percentage, int randomize)
std::vector<int> CFITPOD::select(int n, double fraction, int randomize)
{
std::vector<int> selected;
int m = (int) std::round(n*percentage);
int m = (int) std::round(n*fraction);
m = MAX(m, 1);
selected = (randomize==1) ? shuffle(1, n, m) : linspace(1, n, m);
@ -602,14 +602,14 @@ std::vector<int> CFITPOD::select(int n, double percentage, int randomize)
void CFITPOD::select_data(datastruct &newdata, datastruct data)
{
double percentage = data.percentage;
double fraction = data.fraction;
int randomize = data.randomize;
if (comm->me == 0) {
if (randomize==1)
utils::logmesg(lmp, "Select {} percent of the data set at random using shuffle\n", data.percentage*100);
utils::logmesg(lmp, "Select {} fraction of the data set at random using shuffle\n", data.fraction);
else
utils::logmesg(lmp, "Select {} percent of the data set deterministically using linspace\n", data.percentage*100);
utils::logmesg(lmp, "Select {} fraction of the data set deterministically using linspace\n", data.fraction);
}
int nfiles = data.data_files.size(); // number of files
@ -621,7 +621,7 @@ void CFITPOD::select_data(datastruct &newdata, datastruct data)
for (int file = 0; file < nfiles; file++) {
int nconfigs = data.num_config[file];
selected[file] = select(nconfigs, percentage, randomize);
selected[file] = select(nconfigs, fraction, randomize);
int ns = (int) selected[file].size(); // number of selected configurations
newdata.num_config[file] = ns;
@ -725,12 +725,12 @@ void CFITPOD::read_data_files(std::string data_file, std::vector<std::string> sp
data.test_analysis = (int) data.fitting_weights[4];
data.training_calculation = (int) data.fitting_weights[5];
data.test_calculation = (int) data.fitting_weights[6];
data.percentage = data.fitting_weights[7];
data.fraction = data.fitting_weights[7];
data.randomize = (int) data.fitting_weights[9];
data.copydatainfo(traindata);
if (data.percentage >= 1.0) {
if (data.fraction >= 1.0) {
if (comm->me == 0)
utils::logmesg(lmp, "**************** Begin of Training Data Set ****************\n");
if ((int) traindata.data_path.size() > 1)
@ -771,7 +771,7 @@ void CFITPOD::read_data_files(std::string data_file, std::vector<std::string> sp
testdata.test_analysis = traindata.test_analysis;
testdata.training_calculation = traindata.training_calculation;
testdata.test_calculation = traindata.test_calculation;
testdata.percentage = traindata.fitting_weights[8];
testdata.fraction = traindata.fitting_weights[8];
testdata.randomize = (int) traindata.fitting_weights[10];
if (comm->me == 0)
utils::logmesg(lmp, "**************** Begin of Test Data Set ****************\n");
@ -1331,7 +1331,7 @@ void CFITPOD::print_analysis(datastruct data, double *outarray, double *errors)
std::string filename_analysis = data.training ? "training_analysis.txt" : "test_analysis.txt";
FILE *fp_errors = fopen(filename_errors.c_str(), "w");
FILE *fp_analysis = fopen(filename_errors.c_str(), "w");
FILE *fp_analysis = fopen(filename_analysis.c_str(), "w");
std::string sa = "**************** Begin of Error Analysis for the Training Data Set ****************";
std::string sb = "**************** Begin of Error Analysis for the Test Data Set ****************";