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Read xyz files with lammps utils

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This commit is contained in:
rohskopf
2022-11-05 19:59:48 -06:00
parent 97a0f0f40a
commit 7d7227c334
2 changed files with 186 additions and 81 deletions
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266
src/ML-POD/compute_podfit.cpp
View File

@ -94,7 +94,7 @@ void CPODFIT::init()
neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);
if (modify->get_compute_by_style("podfit").size() > 1 && comm->me == 0)
error->warning(FLERR,"More than one compute podfit");
error->warning(FLERR,"More than one compute podfit");
// memory->create(coeff, podptr->pod.nd, podptr->pod.nelements+1, "podfit:coeff");
// for (int i=0; i<podptr->pod.nd; i++)
@ -313,23 +313,58 @@ void CPODFIT::get_exyz_files(std::vector<std::string>& files, std::string datapa
int CPODFIT::get_number_atom_exyz(std::vector<int>& num_atom, int& num_atom_sum, std::string file)
{
std::ifstream datafile(file);
if (!datafile) {/*error*/}
std::string line;
std::string filename = file;
FILE *fp;
if (comm->me == 0){
fp = utils::open_potential(filename,lmp,nullptr);
if (fp == nullptr)
error->one(FLERR,"Cannot open POD coefficient file {}: ",
filename, utils::getsyserror());
}
char line[MAXLINE],*ptr;
int eof = 0;
int nwords = 0;
int num_configs = 0;
num_atom_sum = 0;
while (std::getline(datafile, line)) // Read next line to `line`, stop if no more lines.
{
int d;
if (is_a_number(line)) {
d = std::stoi(line);
num_atom.push_back(d);
// loop over all lines of this xyz file and extract number of atoms and number of configs
while (true) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == nullptr) {
eof = 1;
fclose(fp);
}
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world);
// words = ptrs to all words in line
// strip single and double quotes from words
std::vector<std::string> words;
try {
words = Tokenizer(utils::trim_comment(line),"\"' \t\n\r\f").as_vector();
} catch (TokenizerException &) {
// ignore
}
if (words.size() == 0) continue;
int natom;
if (words.size() == 1){
natom = utils::inumeric(FLERR,words[0],false,lmp);
num_atom.push_back(natom);
num_configs += 1;
num_atom_sum += d;
}
}
datafile.close();
num_atom_sum += natom;
}
}
return num_configs;
}
@ -355,76 +390,147 @@ int CPODFIT::get_number_atoms(std::vector<int>& num_atom, std::vector<int> &num_
void CPODFIT::read_exyz_file(double *lattice, double *stress, double *energy, double *pos, double *forces,
int *atomtype, std::string file, std::vector<std::string> species)
{
std::ifstream datafile(file);
if (!datafile) {/*error*/}
std::string substr1 = "nergy";
//std::string substr2 = "ttice";
std::string substr3 = "tress";
std::string filename = file;
FILE *fp;
if (comm->me == 0){
fp = utils::open_potential(filename,lmp,nullptr);
if (fp == nullptr)
error->one(FLERR,"Cannot open POD coefficient file {}: ",
filename, utils::getsyserror());
}
char line[MAXLINE],*ptr;
int eof = 0;
int nwords = 0;
int cfi = 0, nat=0, k = 0, ns = species.size();
double d;
std::string line;
while (std::getline(datafile, line)) // Read next line to `line`, stop if no more lines.
{
if (line.substr(1,6) == "attice") {
int index1 = line.find(substr1);
//int index2 = line.find(substr2);
int index3 = line.find(substr3);
if (line.substr(index1,6) == "nergy=") {
std::string s1 = line.substr(index1+6,-1);
int ind = s1.find(" ");
energy[cfi] = stod(line.substr(index1+6,ind));
// loop over all lines of this xyz file and extract training data
while (true) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == nullptr) {
eof = 1;
fclose(fp);
}
//std::cout<<line<<std::endl;
if (line.substr(1,6) == "attice") {
//std::string s1 = line.substr(0,-1);
int ind1 = line.find("\"");
int ind2 = line.find("\"",ind1+1);
std::istringstream ss(line.substr(ind1+1,ind2-ind1));
//std::cout<<line.substr(ind1+1,ind2-ind1-1)<<std::endl;
k = 0;
while(ss >> d){
lattice[k + 9*cfi] = d;
k += 1;
}
}
if (line.substr(index3,6) == "tress=") {
std::string s1 = line.substr(index3+7,-1);
int ind = s1.find("\"");
std::istringstream ss(line.substr(index3+7,ind));
k = 0;
while(ss >> d){
stress[k + 9*cfi] = d;
k += 1;
}
}
cfi += 1;
}
else if (!is_a_number(line)) {
std::string s0;
std::istringstream ss(line);
ss >> s0;
for (int ii=0; ii<ns; ii++)
if (species[ii] == s0)
atomtype[nat] = ii+1;
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world);
// words = ptrs to all words in line
// strip single and double quotes from words
std::vector<std::string> words;
try {
words = Tokenizer(utils::trim_comment(line),"\"' \t\n\r\f").as_vector();
} catch (TokenizerException &) {
// ignore
}
if (words.size() == 0) continue;
ValueTokenizer text(utils::trim_comment(line),"\"' \t\n\r\f");
if (text.contains("attice")){
// find the word containing "lattice"
auto it = std::find_if(words.begin(), words.end(), [](const std::string& str) { return str.find("attice") != std::string::npos; });
// get index of element from iterator
int index = std::distance(words.begin(), it);
if (words[index].find("=") != std::string::npos) {
// lattice numbers start at index + 1
for (int k = 0; k < 9; k++){
lattice[k + 9*cfi] = utils::numeric(FLERR,words[index+1+k],false,lmp);
}
}
else{
// lattice numbers start at index + 2
for (int k = 0; k < 9; k++){
lattice[k + 9*cfi] = utils::numeric(FLERR,words[index+2+k],false,lmp);
}
}
// find the word containing "energy"
it = std::find_if(words.begin(), words.end(), [](const std::string& str) { return str.find("nergy") != std::string::npos; });
// get index of element from iterator
index = std::distance(words.begin(), it);
if (words[index].find("=") != std::string::npos) {
// energy is after "=" inside this string
std::size_t found = words[index].find("=");
energy[cfi] = utils::numeric(FLERR,words[index].substr(found+1),false,lmp);
}
else{
// energy is at index + 2
energy[cfi] = utils::numeric(FLERR,words[index+2],false,lmp);
}
// find the word containing "stress"
it = std::find_if(words.begin(), words.end(), [](const std::string& str) { return str.find("tress") != std::string::npos; });
// get index of element from iterator
index = std::distance(words.begin(), it);
if (words[index].find("=") != std::string::npos) {
// lattice numbers start at index + 1
for (int k = 0; k < 9; k++){
stress[k + 9*cfi] = utils::numeric(FLERR,words[index+1+k],false,lmp);
}
}
else{
// lattice numbers start at index + 2
k = 0;
while(ss >> d){
if (k <=2 ) pos[k + 3*nat] = d;
if (k > 2 ) forces[k-3 + 3*nat] = d;
k += 1;
}
nat += 1;
}
}
datafile.close();
for (int k = 0; k < 9; k++){
stress[k + 9*cfi] = utils::numeric(FLERR,words[index+2+k],false,lmp);
}
}
cfi += 1;
}
// loop over atoms
else if (words.size() > 1){
for (int ii = 0; ii < ns; ii++)
if (species[ii] == words[0])
atomtype[nat] = ii+1;
for (int k = 0; k < 6; k++){
if (k <= 2) pos[k + 3*nat] = utils::numeric(FLERR,words[1+k],false,lmp);
if (k > 2 ) forces[k-3 + 3*nat] = utils::numeric(FLERR,words[1+k],false,lmp);
}
nat += 1;
}
}
}
void CPODFIT::get_data(datastruct &data, std::vector<std::string> species)

1
src/ML-POD/pod.cpp
View File

@ -734,7 +734,6 @@ void CPOD::read_coeff_file(std::string coeff_file)
// strip comment, skip line if blank
nwords = utils::count_words(utils::trim_comment(line));
printf("nwords: %d\n", nwords);
}
if (nwords != 2)