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Update pair eim

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This commit is contained in:
Richard Berger
2020-05-29 14:58:04 -04:00
parent 10b0d60709
commit 1375c154f9
4 changed files with 515 additions and 182 deletions
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433
src/MANYBODY/pair_eim.cpp
View File

@ -27,11 +27,11 @@
#include "memory.h" #include "memory.h"
#include "error.h" #include "error.h"
#include "utils.h" #include "utils.h"
#include "tokenizer.h"
#include "potential_file_reader.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
#define MAXLINE 1024
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
PairEIM::PairEIM(LAMMPS *lmp) : Pair(lmp) PairEIM::PairEIM(LAMMPS *lmp) : Pair(lmp)
@ -451,20 +451,6 @@ double PairEIM::init_one(int i, int j)
void PairEIM::read_file(char *filename) void PairEIM::read_file(char *filename)
{ {
// open potential file
int me = comm->me;
FILE *fptr;
if (me == 0) {
fptr = force->open_potential(filename);
if (fptr == NULL) {
char str[128];
snprintf(str,128,"Cannot open EIM potential file %s",filename);
error->one(FLERR,str);
}
}
int npair = nelements*(nelements+1)/2; int npair = nelements*(nelements+1)/2;
setfl->ielement = new int[nelements]; setfl->ielement = new int[nelements];
setfl->mass = new double[nelements]; setfl->mass = new double[nelements];
@ -488,52 +474,55 @@ void PairEIM::read_file(char *filename)
setfl->rs = new double[npair]; setfl->rs = new double[npair];
setfl->tp = new int[npair]; setfl->tp = new int[npair];
if (me == 0) // read potential file
if (!grabglobal(fptr)) if( comm->me == 0) {
error->one(FLERR,"Could not grab global entry from EIM potential file"); EIMPotentialFileReader reader(lmp, filename);
MPI_Bcast(&setfl->division,1,MPI_DOUBLE,0,world);
MPI_Bcast(&setfl->rbig,1,MPI_DOUBLE,0,world);
MPI_Bcast(&setfl->rsmall,1,MPI_DOUBLE,0,world);
for (int i = 0; i < nelements; i++) { reader.get_global(setfl);
if (me == 0)
if (!grabsingle(fptr,i))
error->one(FLERR,"Could not grab element entry from EIM potential file");
MPI_Bcast(&setfl->ielement[i],1,MPI_INT,0,world);
MPI_Bcast(&setfl->mass[i],1,MPI_DOUBLE,0,world);
MPI_Bcast(&setfl->negativity[i],1,MPI_DOUBLE,0,world);
MPI_Bcast(&setfl->ra[i],1,MPI_DOUBLE,0,world);
MPI_Bcast(&setfl->ri[i],1,MPI_DOUBLE,0,world);
MPI_Bcast(&setfl->Ec[i],1,MPI_DOUBLE,0,world);
MPI_Bcast(&setfl->q0[i],1,MPI_DOUBLE,0,world);
}
for (int i = 0; i < nelements; i++) { for (int i = 0; i < nelements; i++) {
for (int j = i; j < nelements; j++) { reader.get_element(setfl, i, elements[i]);
int ij; }
if (i == j) ij = i;
else if (i < j) ij = nelements*(i+1) - (i+1)*(i+2)/2 + j; for (int i = 0; i < nelements; i++) {
else ij = nelements*(j+1) - (j+1)*(j+2)/2 + i; for (int j = i; j < nelements; j++) {
if (me == 0) int ij;
if (grabpair(fptr,i,j) == 0) if (i == j) ij = i;
error->one(FLERR,"Could not grab pair entry from EIM potential file"); else if (i < j) ij = nelements*(i+1) - (i+1)*(i+2)/2 + j;
MPI_Bcast(&setfl->rcutphiA[ij],1,MPI_DOUBLE,0,world); else ij = nelements*(j+1) - (j+1)*(j+2)/2 + i;
MPI_Bcast(&setfl->rcutphiR[ij],1,MPI_DOUBLE,0,world); reader.get_pair(setfl, ij, elements[i], elements[j]);
MPI_Bcast(&setfl->Eb[ij],1,MPI_DOUBLE,0,world); }
MPI_Bcast(&setfl->r0[ij],1,MPI_DOUBLE,0,world);
MPI_Bcast(&setfl->alpha[ij],1,MPI_DOUBLE,0,world);
MPI_Bcast(&setfl->beta[ij],1,MPI_DOUBLE,0,world);
MPI_Bcast(&setfl->rcutq[ij],1,MPI_DOUBLE,0,world);
MPI_Bcast(&setfl->Asigma[ij],1,MPI_DOUBLE,0,world);
MPI_Bcast(&setfl->rq[ij],1,MPI_DOUBLE,0,world);
MPI_Bcast(&setfl->rcutsigma[ij],1,MPI_DOUBLE,0,world);
MPI_Bcast(&setfl->Ac[ij],1,MPI_DOUBLE,0,world);
MPI_Bcast(&setfl->zeta[ij],1,MPI_DOUBLE,0,world);
MPI_Bcast(&setfl->rs[ij],1,MPI_DOUBLE,0,world);
MPI_Bcast(&setfl->tp[ij],1,MPI_INT,0,world);
} }
} }
// broadcast potential information to other procs
MPI_Bcast(&setfl->division, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&setfl->rbig, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&setfl->rsmall, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(setfl->ielement, nelements, MPI_INT, 0, world);
MPI_Bcast(setfl->mass, nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(setfl->negativity, nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(setfl->ra, nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(setfl->ri, nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(setfl->Ec, nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(setfl->q0, nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(setfl->rcutphiA, npair, MPI_DOUBLE, 0, world);
MPI_Bcast(setfl->rcutphiR, npair, MPI_DOUBLE, 0, world);
MPI_Bcast(setfl->Eb, npair, MPI_DOUBLE, 0, world);
MPI_Bcast(setfl->r0, npair, MPI_DOUBLE, 0, world);
MPI_Bcast(setfl->alpha, npair, MPI_DOUBLE, 0, world);
MPI_Bcast(setfl->beta, npair, MPI_DOUBLE, 0, world);
MPI_Bcast(setfl->rcutq, npair, MPI_DOUBLE, 0, world);
MPI_Bcast(setfl->Asigma, npair, MPI_DOUBLE, 0, world);
MPI_Bcast(setfl->rq, npair, MPI_DOUBLE, 0, world);
MPI_Bcast(setfl->rcutsigma, npair, MPI_DOUBLE, 0, world);
MPI_Bcast(setfl->Ac, npair, MPI_DOUBLE, 0, world);
MPI_Bcast(setfl->zeta, npair, MPI_DOUBLE, 0, world);
MPI_Bcast(setfl->rs, npair, MPI_DOUBLE, 0, world);
MPI_Bcast(setfl->tp, npair, MPI_INT, 0, world);
setfl->nr = 5000; setfl->nr = 5000;
setfl->cut = 0.0; setfl->cut = 0.0;
for (int i = 0; i < npair; i++) { for (int i = 0; i < npair; i++) {
@ -602,10 +591,6 @@ void PairEIM::read_file(char *filename)
} }
} }
} }
// close the potential file
if (me == 0) fclose(fptr);
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -879,114 +864,6 @@ void PairEIM::interpolate(int n, double delta, double *f,
} }
} }
/* ----------------------------------------------------------------------
grab global line from file and store info in setfl
return 0 if error
------------------------------------------------------------------------- */
int PairEIM::grabglobal(FILE *fptr)
{
char line[MAXLINE];
char *pch = NULL, *data = NULL;
while (pch == NULL) {
if (fgets(line,MAXLINE,fptr) == NULL) break;
pch = strstr(line,"global");
if (pch != NULL) {
data = strtok (line," \t\n\r\f");
data = strtok (NULL,"?");
sscanf(data,"%lg %lg %lg",&setfl->division,&setfl->rbig,&setfl->rsmall);
}
}
if (pch == NULL) return 0;
return 1;
}
/* ----------------------------------------------------------------------
grab elemental line from file and store info in setfl
return 0 if error
------------------------------------------------------------------------- */
int PairEIM::grabsingle(FILE *fptr, int i)
{
char line[MAXLINE];
rewind(fptr);
char *pch1 = NULL, *pch2 = NULL, *data = NULL;
while (pch1 == NULL || pch2 == NULL) {
if (fgets(line,MAXLINE,fptr) == NULL) break;
pch1 = strtok (line," \t\n\r\f");
pch1 = strstr(pch1,"element:");
if (pch1 != NULL) {
pch2 = strtok(NULL, " \t\n\r\f");
if (pch2 != NULL) {
data = strtok (NULL, "?");
if (strcmp(pch2,elements[i]) == 0) {
sscanf(data,"%d %lg %lg %lg %lg %lg %lg",&setfl->ielement[i],
&setfl->mass[i],&setfl->negativity[i],&setfl->ra[i],
&setfl->ri[i],&setfl->Ec[i],&setfl->q0[i]);
} else pch2 = NULL;
}
}
}
if (pch1 == NULL || pch2 == NULL) return 0;
return 1;
}
/* ----------------------------------------------------------------------
grab pair line from file and store info in setfl
return 0 if error
------------------------------------------------------------------------- */
int PairEIM::grabpair(FILE *fptr, int i, int j)
{
char line[MAXLINE];
rewind(fptr);
int ij;
if (i == j) ij = i;
else if (i < j) ij = nelements*(i+1) - (i+1)*(i+2)/2 + j;
else ij = nelements*(j+1) - (j+1)*(j+2)/2 + i;
char *pch1 = NULL, *pch2 = NULL, *pch3 = NULL, *data = NULL;
while (pch1 == NULL || pch2 == NULL || pch3 == NULL) {
if (fgets(line,MAXLINE,fptr) == NULL) break;
pch1 = strtok (line," \t\n\r\f");
pch1 = strstr(pch1,"pair:");
if (pch1 != NULL) {
pch2 = strtok (NULL, " \t\n\r\f");
if (pch2 != NULL) pch3 = strtok (NULL, " \t\n\r\f");
if (pch3 != NULL) data = strtok (NULL, "?");
if ((pch2 != NULL) && (pch3 != NULL)) {
if ((strcmp(pch2,elements[i]) == 0 &&
strcmp(pch3,elements[j]) == 0) ||
(strcmp(pch2,elements[j]) == 0 &&
strcmp(pch3,elements[i]) == 0)) {
sscanf(data,"%lg %lg %lg %lg %lg",
&setfl->rcutphiA[ij],&setfl->rcutphiR[ij],
&setfl->Eb[ij],&setfl->r0[ij],&setfl->alpha[ij]);
utils::sfgets(FLERR,line,MAXLINE,fptr,NULL,error);
sscanf(line,"%lg %lg %lg %lg %lg",
&setfl->beta[ij],&setfl->rcutq[ij],&setfl->Asigma[ij],
&setfl->rq[ij],&setfl->rcutsigma[ij]);
utils::sfgets(FLERR,line,MAXLINE,fptr,NULL,error);
sscanf(line,"%lg %lg %lg %d",
&setfl->Ac[ij],&setfl->zeta[ij],&setfl->rs[ij],
&setfl->tp[ij]);
} else {
pch1 = NULL;
pch2 = NULL;
pch3 = NULL;
}
}
}
}
if (pch1 == NULL || pch2 == NULL || pch3 == NULL) return 0;
return 1;
}
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
cutoff function cutoff function
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
@ -1171,3 +1048,221 @@ double PairEIM::memory_usage()
bytes += 2 * nmax * sizeof(double); bytes += 2 * nmax * sizeof(double);
return bytes; return bytes;
} }
EIMPotentialFileReader::EIMPotentialFileReader(LAMMPS * lmp, const std::string & filename) :
Pointers(lmp), filename(filename)
{
if (comm->me != 0) {
error->one(FLERR, "EIMPotentialFileReader should only be called by proc 0!");
}
FILE * fp = force->open_potential(filename.c_str());
if (fp == NULL) {
char str[128];
snprintf(str, 128, "cannot open EIM potential file %s", filename.c_str());
error->one(FLERR, str);
}
parse(fp);
fclose(fp);
}
std::pair<std::string, std::string> EIMPotentialFileReader::get_pair(const std::string & a, const std::string & b) {
if (a < b) {
return std::make_pair(a, b);
}
return std::make_pair(b, a);
}
char * EIMPotentialFileReader::next_line(FILE * fp) {
// concatenate lines if they end with '&'
// strip comments after '#'
int n = 0;
int nwords = 0;
bool concat = false;
char *ptr = fgets(line, MAXLINE, fp);
if (ptr == nullptr) {
// EOF
return nullptr;
}
// strip comment
if ((ptr = strchr(line, '#'))) *ptr = '\0';
// strip ampersand
if ((ptr = strrchr(line, '&'))) {
concat = true;
*ptr = '\0';
}
nwords = utils::count_words(line);
if (nwords > 0) {
n = strlen(line);
}
while(n == 0 || concat) {
char *ptr = fgets(&line[n], MAXLINE - n, fp);
if (ptr == nullptr) {
// EOF
return line;
}
// strip comment
if ((ptr = strchr(line, '#'))) *ptr = '\0';
// strip ampersand
if ((ptr = strrchr(line, '&'))) {
concat = true;
*ptr = '\0';
} else {
concat = false;
}
nwords = utils::count_words(line);
// skip line if blank
if (nwords > 0) {
n = strlen(line);
}
}
return line;
}
void EIMPotentialFileReader::parse(FILE * fp)
{
char * line = nullptr;
bool found_global = false;
while(line = next_line(fp)) {
ValueTokenizer values(line, " \t\r\n\f");
std::string type = values.next_string();
if (type == "global:") {
if (values.count() != 4) {
error->one(FLERR, "Invalid global line in EIM potential file");
}
division = values.next_double();
rbig = values.next_double();
rsmall = values.next_double();
found_global = true;
} else if (type == "element:") {
if (values.count() != 9) {
error->one(FLERR, "Invalid element line in EIM potential file");
}
std::string name = values.next_string();
ElementData data;
data.ielement = values.next_int();
data.mass = values.next_double();
data.negativity = values.next_double();
data.ra = values.next_double();
data.ri = values.next_double();
data.Ec = values.next_double();
data.q0 = values.next_double();
if (elements.find(name) == elements.end()) {
elements[name] = data;
} else {
error->one(FLERR, "Duplicate pair line in EIM potential file");
}
} else if (type == "pair:") {
if (values.count() != 17) {
error->one(FLERR, "Invalid element line in EIM potential file");
}
std::string elementA = values.next_string();
std::string elementB = values.next_string();
PairData data;
data.rcutphiA = values.next_double();
data.rcutphiR = values.next_double();
data.Eb = values.next_double();
data.r0 = values.next_double();
data.alpha = values.next_double();
data.beta = values.next_double();
data.rcutq = values.next_double();
data.Asigma = values.next_double();
data.rq = values.next_double();
data.rcutsigma = values.next_double();
data.Ac = values.next_double();
data.zeta = values.next_double();
data.rs = values.next_double();
// should be next_int, but since existing potential files have 1.0000e+00 format
// we're doing this instead to keep compatibility
data.tp = (int)values.next_double();
auto p = get_pair(elementA, elementB);
if (pairs.find(p) == pairs.end()) {
pairs[p] = data;
} else {
error->one(FLERR, "Duplicate pair line in EIM potential file");
}
}
}
if (!found_global) {
error->one(FLERR, "Missing global line in EIM potential file");
}
}
void EIMPotentialFileReader::get_global(PairEIM::Setfl * setfl) {
setfl->division = division;
setfl->rbig = rbig;
setfl->rsmall = rsmall;
}
void EIMPotentialFileReader::get_element(PairEIM::Setfl * setfl, int i, const std::string & name) {
if (elements.find(name) == elements.end()) {
char str[128];
snprintf(str, 128, "Element %s not defined in EIM potential file", name.c_str());
error->one(FLERR, str);
}
ElementData & data = elements[name];
setfl->ielement[i] = data.ielement;
setfl->mass[i] = data.mass;
setfl->negativity[i] = data.negativity;
setfl->ra[i] = data.ra;
setfl->ri[i] = data.ri;
setfl->Ec[i] = data.Ec;
setfl->q0[i] = data.q0;
}
void EIMPotentialFileReader::get_pair(PairEIM::Setfl * setfl, int ij, const std::string & elemA, const std::string & elemB) {
auto p = get_pair(elemA, elemB);
if (pairs.find(p) == pairs.end()) {
char str[128];
snprintf(str, 128, "Pair (%s, %s) not defined in EIM potential file", elemA.c_str(), elemB.c_str());
error->one(FLERR, str);
}
PairData & data = pairs[p];
setfl->rcutphiA[ij] = data.rcutphiA;
setfl->rcutphiR[ij] = data.rcutphiR;
setfl->Eb[ij] = data.Eb;
setfl->r0[ij] = data.r0;
setfl->alpha[ij] = data.alpha;
setfl->beta[ij] = data.beta;
setfl->rcutq[ij] = data.rcutq;
setfl->Asigma[ij] = data.Asigma;
setfl->rq[ij] = data.rq;
setfl->rcutsigma[ij] = data.rcutsigma;
setfl->Ac[ij] = data.Ac;
setfl->zeta[ij] = data.zeta;
setfl->rs[ij] = data.rs;
setfl->tp[ij] = data.tp;
}

79
src/MANYBODY/pair_eim.h
View File

@ -21,6 +21,8 @@ PairStyle(eim,PairEIM)
#define LMP_PAIR_EIM_H #define LMP_PAIR_EIM_H
#include "pair.h" #include "pair.h"
#include <string>
#include <map>
namespace LAMMPS_NS { namespace LAMMPS_NS {
@ -40,16 +42,6 @@ class PairEIM : public Pair {
void unpack_reverse_comm(int, int *, double *); void unpack_reverse_comm(int, int *, double *);
double memory_usage(); double memory_usage();
protected:
double **cutforcesq,cutmax;
int nmax;
double *rho,*fp;
int rhofp;
int *map; // which element each atom type maps to
int nelements; // # of elements to read from potential file
char **elements; // element names
struct Setfl { struct Setfl {
double division,rbig,rsmall; double division,rbig,rsmall;
int nr; int nr;
@ -62,6 +54,17 @@ class PairEIM : public Pair {
double ***Fij,***Gij,***phiij; double ***Fij,***Gij,***phiij;
double **cuts; double **cuts;
}; };
protected:
double **cutforcesq,cutmax;
int nmax;
double *rho,*fp;
int rhofp;
int *map; // which element each atom type maps to
int nelements; // # of elements to read from potential file
char **elements; // element names
Setfl *setfl; Setfl *setfl;
// potentials as array data // potentials as array data
@ -80,9 +83,6 @@ class PairEIM : public Pair {
void allocate(); void allocate();
void array2spline(); void array2spline();
void interpolate(int, double, double *, double **, double); void interpolate(int, double, double *, double **, double);
int grabglobal(FILE *);
int grabsingle(FILE *, int);
int grabpair(FILE *, int, int);
double funccutoff(double, double, double); double funccutoff(double, double, double);
double funcphi(int, int, double); double funcphi(int, int, double);
@ -94,6 +94,59 @@ class PairEIM : public Pair {
void file2array(); void file2array();
}; };
class EIMPotentialFileReader : protected Pointers {
std::string filename;
static const int MAXLINE = 1024;
char line[MAXLINE];
void parse(FILE * fp);
char * next_line(FILE * fp);
std::pair<std::string, std::string> get_pair(const std::string & a, const std::string & b);
public:
EIMPotentialFileReader(class LAMMPS* lmp, const std::string & filename);
void get_global(PairEIM::Setfl * setfl);
void get_element(PairEIM::Setfl * setfl, int i, const std::string & name);
void get_pair(PairEIM::Setfl * setfl, int ij, const std::string & elemA, const std::string & elemB);
private:
// potential parameters
double division;
double rbig;
double rsmall;
struct ElementData {
int ielement;
double mass;
double negativity;
double ra;
double ri;
double Ec;
double q0;
};
struct PairData {
double rcutphiA;
double rcutphiR;
double Eb;
double r0;
double alpha;
double beta;
double rcutq;
double Asigma;
double rq;
double rcutsigma;
double Ac;
double zeta;
double rs;
int tp;
};
std::map<std::string, ElementData> elements;
std::map<std::pair<std::string,std::string>, PairData> pairs;
};
} }
#endif #endif

7
unittest/formats/CMakeLists.txt
View File

@ -2,3 +2,10 @@ add_executable(test_potential_file_reader test_potential_file_reader.cpp)
target_link_libraries(test_potential_file_reader PRIVATE lammps GTest::GMock GTest::GTest) target_link_libraries(test_potential_file_reader PRIVATE lammps GTest::GMock GTest::GTest)
add_test(NAME PotentialFileReader COMMAND test_potential_file_reader WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) add_test(NAME PotentialFileReader COMMAND test_potential_file_reader WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
set_tests_properties(PotentialFileReader PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}") set_tests_properties(PotentialFileReader PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
if (PKG_MANYBODY)
add_executable(test_eim_potential_file_reader test_eim_potential_file_reader.cpp)
target_link_libraries(test_eim_potential_file_reader PRIVATE lammps GTest::GMock GTest::GTest)
add_test(NAME EIMPotentialFileReader COMMAND test_eim_potential_file_reader WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
set_tests_properties(EIMPotentialFileReader PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
endif()

178
unittest/formats/test_eim_potential_file_reader.cpp Normal file
View File

@ -0,0 +1,178 @@
#include "gmock/gmock.h"
#include "gtest/gtest.h"
#include "lammps.h"
#include "utils.h"
#include "MANYBODY/pair_eim.h"
#include <mpi.h>
using namespace LAMMPS_NS;
class EIMPotentialFileReaderTest : public ::testing::Test {
protected:
LAMMPS * lmp;
PairEIM::Setfl setfl;
static const int nelements = 9;
void SetUp() override {
const char *args[] = {"PotentialFileReaderTest", "-log", "none", "-echo", "screen", "-nocite" };
char **argv = (char **)args;
int argc = sizeof(args)/sizeof(char *);
::testing::internal::CaptureStdout();
lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD);
::testing::internal::GetCapturedStdout();
int npair = nelements*(nelements+1)/2;
setfl.ielement = new int[nelements];
setfl.mass = new double[nelements];
setfl.negativity = new double[nelements];
setfl.ra = new double[nelements];
setfl.ri = new double[nelements];
setfl.Ec = new double[nelements];
setfl.q0 = new double[nelements];
setfl.rcutphiA = new double[npair];
setfl.rcutphiR = new double[npair];
setfl.Eb = new double[npair];
setfl.r0 = new double[npair];
setfl.alpha = new double[npair];
setfl.beta = new double[npair];
setfl.rcutq = new double[npair];
setfl.Asigma = new double[npair];
setfl.rq = new double[npair];
setfl.rcutsigma = new double[npair];
setfl.Ac = new double[npair];
setfl.zeta = new double[npair];
setfl.rs = new double[npair];
setfl.tp = new int[npair];
}
void TearDown() override {
delete [] setfl.ielement;
delete [] setfl.mass;
delete [] setfl.negativity;
delete [] setfl.ra;
delete [] setfl.ri;
delete [] setfl.Ec;
delete [] setfl.q0;
delete [] setfl.rcutphiA;
delete [] setfl.rcutphiR;
delete [] setfl.Eb;
delete [] setfl.r0;
delete [] setfl.alpha;
delete [] setfl.beta;
delete [] setfl.rcutq;
delete [] setfl.Asigma;
delete [] setfl.rq;
delete [] setfl.rcutsigma;
delete [] setfl.Ac;
delete [] setfl.zeta;
delete [] setfl.rs;
delete [] setfl.tp;
::testing::internal::CaptureStdout();
delete lmp;
::testing::internal::GetCapturedStdout();
}
};
TEST_F(EIMPotentialFileReaderTest, global_line) {
::testing::internal::CaptureStdout();
EIMPotentialFileReader reader(lmp, "ffield.eim");
::testing::internal::GetCapturedStdout();
reader.get_global(&setfl);
ASSERT_DOUBLE_EQ(setfl.division, 2.0);
ASSERT_DOUBLE_EQ(setfl.rbig, -1.645);
ASSERT_DOUBLE_EQ(setfl.rsmall, 1.645);
}
TEST_F(EIMPotentialFileReaderTest, element_line_sequential) {
::testing::internal::CaptureStdout();
EIMPotentialFileReader reader(lmp, "ffield.eim");
::testing::internal::GetCapturedStdout();
reader.get_element(&setfl, 0, "Li");
ASSERT_EQ(setfl.ielement[0], 3);
ASSERT_DOUBLE_EQ(setfl.mass[0], 6.9410e+00);
ASSERT_DOUBLE_EQ(setfl.negativity[0], 9.8000e-01);
ASSERT_DOUBLE_EQ(setfl.ra[0], 1.1220e+00);
ASSERT_DOUBLE_EQ(setfl.ri[0], 1.1220e+00);
ASSERT_DOUBLE_EQ(setfl.Ec[0], -1.6500e+00);
ASSERT_DOUBLE_EQ(setfl.q0[0], 0.0000e+00);
reader.get_element(&setfl, 1, "Na");
ASSERT_EQ(setfl.ielement[1], 11);
ASSERT_DOUBLE_EQ(setfl.mass[1], 2.2990e+01);
ASSERT_DOUBLE_EQ(setfl.negativity[1], 9.3000e-01);
ASSERT_DOUBLE_EQ(setfl.ra[1], 1.3690e+00);
ASSERT_DOUBLE_EQ(setfl.ri[1], 1.3690e+00);
ASSERT_DOUBLE_EQ(setfl.Ec[1], -1.1100e+00);
ASSERT_DOUBLE_EQ(setfl.q0[1], 0.0000e+00);
}
TEST_F(EIMPotentialFileReaderTest, element_line_random) {
::testing::internal::CaptureStdout();
EIMPotentialFileReader reader(lmp, "ffield.eim");
::testing::internal::GetCapturedStdout();
reader.get_element(&setfl, 0, "Id");
ASSERT_EQ(setfl.ielement[0], 53);
ASSERT_DOUBLE_EQ(setfl.mass[0], 1.2690e+02);
ASSERT_DOUBLE_EQ(setfl.negativity[0], 2.6600e+00);
ASSERT_DOUBLE_EQ(setfl.ra[0], 1.8500e+00);
ASSERT_DOUBLE_EQ(setfl.ri[0], 1.8500e+00);
ASSERT_DOUBLE_EQ(setfl.Ec[0], -1.1100e+00);
ASSERT_DOUBLE_EQ(setfl.q0[0], 0.0000e+00);
}
TEST_F(EIMPotentialFileReaderTest, pair_line) {
::testing::internal::CaptureStdout();
EIMPotentialFileReader reader(lmp, "ffield.eim");
::testing::internal::GetCapturedStdout();
reader.get_pair(&setfl, 0, "Li", "Li");
ASSERT_DOUBLE_EQ(setfl.rcutphiA[0], 6.0490e+00);
ASSERT_DOUBLE_EQ(setfl.rcutphiR[0], 6.0490e+00);
ASSERT_DOUBLE_EQ(setfl.Eb[0], -2.5330e-01);
ASSERT_DOUBLE_EQ(setfl.r0[0], 3.6176e+00);
ASSERT_DOUBLE_EQ(setfl.alpha[0], 7.5536e+00);
ASSERT_DOUBLE_EQ(setfl.beta[0], 3.5017e+00);
ASSERT_DOUBLE_EQ(setfl.rcutq[0], 0.0000e+00);
ASSERT_DOUBLE_EQ(setfl.Asigma[0], 2.1778e-02);
ASSERT_DOUBLE_EQ(setfl.rq[0], 2.0000e+00);
ASSERT_DOUBLE_EQ(setfl.rcutsigma[0], 7.0637e+00);
ASSERT_DOUBLE_EQ(setfl.Ac[0], 3.3271e-01);
ASSERT_DOUBLE_EQ(setfl.zeta[0], 6.0000e-01);
ASSERT_DOUBLE_EQ(setfl.rs[0], 2.0000e+00);
ASSERT_EQ(setfl.tp[0], 1);
}
TEST_F(EIMPotentialFileReaderTest, pair_identical) {
::testing::internal::CaptureStdout();
EIMPotentialFileReader reader(lmp, "ffield.eim");
::testing::internal::GetCapturedStdout();
reader.get_pair(&setfl, 0, "Li", "Na");
reader.get_pair(&setfl, 1, "Na", "Li");
ASSERT_DOUBLE_EQ(setfl.rcutphiA[0], setfl.rcutphiA[1]);
ASSERT_DOUBLE_EQ(setfl.rcutphiR[0], setfl.rcutphiR[1]);
ASSERT_DOUBLE_EQ(setfl.Eb[0], setfl.Eb[1]);
ASSERT_DOUBLE_EQ(setfl.r0[0], setfl.r0[1]);
ASSERT_DOUBLE_EQ(setfl.alpha[0], setfl.alpha[1]);
ASSERT_DOUBLE_EQ(setfl.beta[0], setfl.beta[1]);
ASSERT_DOUBLE_EQ(setfl.rcutq[0], setfl.rcutq[1]);
ASSERT_DOUBLE_EQ(setfl.Asigma[0], setfl.Asigma[1]);
ASSERT_DOUBLE_EQ(setfl.rq[0], setfl.rq[1]);
ASSERT_DOUBLE_EQ(setfl.rcutsigma[0], setfl.rcutsigma[1]);
ASSERT_DOUBLE_EQ(setfl.Ac[0], setfl.Ac[1]);
ASSERT_DOUBLE_EQ(setfl.zeta[0], setfl.zeta[1]);
ASSERT_DOUBLE_EQ(setfl.rs[0], setfl.rs[1]);
ASSERT_EQ(setfl.tp[0], setfl.tp[1]);
}
int main(int argc, char **argv)
{
MPI_Init(&argc, &argv);
::testing::InitGoogleMock(&argc, argv);
return RUN_ALL_TESTS();
}