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Update pair nb3b harmonic

This commit is contained in:
Richard Berger 2020-05-28 16:05:02 -04:00
parent e206647717
commit cadc374e0b
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GPG Key ID: A9E83994E0BA0CAB
3 changed files with 69 additions and 99 deletions
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147
src/MANYBODY/pair_nb3b_harmonic.cpp
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@ -30,10 +30,11 @@
#include "memory.h"
#include "error.h"
#include "utils.h"
#include "tokenizer.h"
#include "potential_file_reader.h"
using namespace LAMMPS_NS;
#define MAXLINE 1024
#define DELTA 4
#define SMALL 0.001
#define PI 3.141592653589793238462643383279
@ -283,117 +284,73 @@ double PairNb3bHarmonic::init_one(int i, int j)
void PairNb3bHarmonic::read_file(char *file)
{
int params_per_line = 6;
char **words = new char*[params_per_line+1];
memory->sfree(params);
params = NULL;
params = nullptr;
nparams = maxparam = 0;
// open file on proc 0
FILE *fp = NULL;
if (comm->me == 0) {
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
snprintf(str,128,"Cannot open nb3b/harmonic potential file %s",file);
error->one(FLERR,str);
}
}
PotentialFileReader reader(lmp, file, "nb3b/harmonic");
char * line;
// read each set of params from potential file
// one set of params can span multiple lines
// store params if all 3 element tags are in element list
while(line = reader.next_line(NPARAMS_PER_LINE)) {
try {
ValueTokenizer values(line, " \t\n\r\f");
int n,nwords,ielement,jelement,kelement;
char line[MAXLINE],*ptr;
int eof = 0;
std::string iname = values.next_string();
std::string jname = values.next_string();
std::string kname = values.next_string();
while (1) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) {
eof = 1;
fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
// ielement,jelement,kelement = 1st args
// if all 3 args are in element list, then parse this line
// else skip to next entry in file
int ielement, jelement, kelement;
// strip comment, skip line if blank
for (ielement = 0; ielement < nelements; ielement++)
if (iname == elements[ielement]) break;
if (ielement == nelements) continue;
for (jelement = 0; jelement < nelements; jelement++)
if (jname == elements[jelement]) break;
if (jelement == nelements) continue;
for (kelement = 0; kelement < nelements; kelement++)
if (kname == elements[kelement]) break;
if (kelement == nelements) continue;
if ((ptr = strchr(line,'#'))) *ptr = '\0';
nwords = utils::count_words(line);
if (nwords == 0) continue;
// load up parameter settings and error check their values
// concatenate additional lines until have params_per_line words
if (nparams == maxparam) {
maxparam += DELTA;
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
"pair:params");
}
while (nwords < params_per_line) {
n = strlen(line);
if (comm->me == 0) {
ptr = fgets(&line[n],MAXLINE-n,fp);
if (ptr == NULL) {
eof = 1;
fclose(fp);
} else n = strlen(line) + 1;
params[nparams].ielement = ielement;
params[nparams].jelement = jelement;
params[nparams].kelement = kelement;
params[nparams].k_theta = values.next_double();
params[nparams].theta0 = values.next_double();
params[nparams].cutoff = values.next_double();
} catch (TokenizerException & e) {
error->one(FLERR, e.what());
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
if ((ptr = strchr(line,'#'))) *ptr = '\0';
nwords = utils::count_words(line);
if (params[nparams].k_theta < 0.0 || params[nparams].theta0 < 0.0 ||
params[nparams].cutoff < 0.0)
error->one(FLERR,"Illegal nb3b/harmonic parameter");
nparams++;
}
if (nwords != params_per_line)
error->all(FLERR,"Incorrect format in nb3b/harmonic potential file");
// words = ptrs to all words in line
nwords = 0;
words[nwords++] = strtok(line," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
// ielement,jelement,kelement = 1st args
// if all 3 args are in element list, then parse this line
// else skip to next entry in file
for (ielement = 0; ielement < nelements; ielement++)
if (strcmp(words[0],elements[ielement]) == 0) break;
if (ielement == nelements) continue;
for (jelement = 0; jelement < nelements; jelement++)
if (strcmp(words[1],elements[jelement]) == 0) break;
if (jelement == nelements) continue;
for (kelement = 0; kelement < nelements; kelement++)
if (strcmp(words[2],elements[kelement]) == 0) break;
if (kelement == nelements) continue;
// load up parameter settings and error check their values
if (nparams == maxparam) {
maxparam += DELTA;
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
"pair:params");
}
params[nparams].ielement = ielement;
params[nparams].jelement = jelement;
params[nparams].kelement = kelement;
params[nparams].k_theta = atof(words[3]);
params[nparams].theta0 = atof(words[4]);
params[nparams].cutoff = atof(words[5]);
if (params[nparams].k_theta < 0.0 || params[nparams].theta0 < 0.0 ||
params[nparams].cutoff < 0.0)
error->all(FLERR,"Illegal nb3b/harmonic parameter");
nparams++;
}
delete [] words;
MPI_Bcast(&nparams, 1, MPI_INT, 0, world);
MPI_Bcast(&maxparam, 1, MPI_INT, 0, world);
if(comm->me != 0) {
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), "pair:params");
}
MPI_Bcast(params, maxparam*sizeof(Param), MPI_BYTE, 0, world);
}
/* ---------------------------------------------------------------------- */

2
src/MANYBODY/pair_nb3b_harmonic.h
View File

@ -34,6 +34,8 @@ class PairNb3bHarmonic : public Pair {
double init_one(int, int);
void init_style();
static const int NPARAMS_PER_LINE = 6;
protected:
struct Param {
double k_theta, theta0, cutoff;

19
unittest/formats/test_potential_file_reader.cpp
View File

@ -12,6 +12,7 @@
#include "MANYBODY/pair_tersoff_zbl.h"
#include "MANYBODY/pair_gw.h"
#include "MANYBODY/pair_gw_zbl.h"
#include "MANYBODY/pair_nb3b_harmonic.h"
#include <mpi.h>
@ -26,6 +27,7 @@ const int LAMMPS_NS::PairTersoffMODC::NPARAMS_PER_LINE;
const int LAMMPS_NS::PairTersoffZBL::NPARAMS_PER_LINE;
const int LAMMPS_NS::PairGW::NPARAMS_PER_LINE;
const int LAMMPS_NS::PairGWZBL::NPARAMS_PER_LINE;
const int LAMMPS_NS::PairNb3bHarmonic::NPARAMS_PER_LINE;
class PotenialFileReaderTest : public ::testing::Test {
protected:
@ -85,7 +87,7 @@ TEST_F(PotenialFileReaderTest, Tersoff) {
TEST_F(PotenialFileReaderTest, TersoffMod) {
::testing::internal::CaptureStdout();
PotentialFileReader reader(lmp, "Si.tersoff.mod", "Tersoff");
PotentialFileReader reader(lmp, "Si.tersoff.mod", "Tersoff/Mod");
::testing::internal::GetCapturedStdout();
auto line = reader.next_line(PairTersoffMOD::NPARAMS_PER_LINE);
@ -94,7 +96,7 @@ TEST_F(PotenialFileReaderTest, TersoffMod) {
TEST_F(PotenialFileReaderTest, TersoffModC) {
::testing::internal::CaptureStdout();
PotentialFileReader reader(lmp, "Si.tersoff.modc", "Tersoff");
PotentialFileReader reader(lmp, "Si.tersoff.modc", "Tersoff/ModC");
::testing::internal::GetCapturedStdout();
auto line = reader.next_line(PairTersoffMODC::NPARAMS_PER_LINE);
@ -103,7 +105,7 @@ TEST_F(PotenialFileReaderTest, TersoffModC) {
TEST_F(PotenialFileReaderTest, TersoffZBL) {
::testing::internal::CaptureStdout();
PotentialFileReader reader(lmp, "SiC.tersoff.zbl", "Tersoff");
PotentialFileReader reader(lmp, "SiC.tersoff.zbl", "Tersoff/ZBL");
::testing::internal::GetCapturedStdout();
auto line = reader.next_line(PairTersoffZBL::NPARAMS_PER_LINE);
@ -121,13 +123,22 @@ TEST_F(PotenialFileReaderTest, GW) {
TEST_F(PotenialFileReaderTest, GWZBL) {
::testing::internal::CaptureStdout();
PotentialFileReader reader(lmp, "SiC.gw.zbl", "GWZBL");
PotentialFileReader reader(lmp, "SiC.gw.zbl", "GW/ZBL");
::testing::internal::GetCapturedStdout();
auto line = reader.next_line(PairGWZBL::NPARAMS_PER_LINE);
ASSERT_EQ(utils::count_words(line), PairGWZBL::NPARAMS_PER_LINE);
}
TEST_F(PotenialFileReaderTest, Nb3bHarmonic) {
::testing::internal::CaptureStdout();
PotentialFileReader reader(lmp, "MOH.nb3b.harmonic", "NB3B Harmonic");
::testing::internal::GetCapturedStdout();
auto line = reader.next_line(PairNb3bHarmonic::NPARAMS_PER_LINE);
ASSERT_EQ(utils::count_words(line), PairNb3bHarmonic::NPARAMS_PER_LINE);
}
int main(int argc, char **argv)
{
MPI_Init(&argc, &argv);