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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14685 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2016-02-26 15:55:15 +00:00
parent 19ca625699
commit b6e19b7803
3 changed files with 197 additions and 23 deletions
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214
src/KIM/pair_kim.cpp
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@ -243,6 +243,10 @@ void PairKIM::allocate()
// allocate standard Pair class arrays
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
// allocate mapping array
@ -282,6 +286,9 @@ void PairKIM::settings(int narg, char **arg)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
// set lmps_* bool flags
set_lmps_flags();
// set virial handling
if (strcmp(arg[0],"LAMMPSvirial") == 0)
{
@ -335,10 +342,9 @@ void PairKIM::coeff(int narg, char **arg)
if (narg != 2 + atom->ntypes)
error->all(FLERR,"Incorrect args for pair coefficients");
// ensure I,J args are * *
if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
error->all(FLERR,"Incorrect args for pair coefficients");
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
// read args that map atom species to KIM elements
// lmps_map_species_to_unique[i] =
@ -374,21 +380,17 @@ void PairKIM::coeff(int narg, char **arg)
}
}
// clear setflag since coeff() called once with I,J = * *
n = atom->ntypes;
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
// set setflag i,j for type pairs where both are mapped to elements
int count = 0;
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
if (lmps_map_species_to_unique[i] >= 0 &&
lmps_map_species_to_unique[j] >= 0) {
setflag[i][j] = 1;
count++;
}
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
if (lmps_map_species_to_unique[i] >= 0 &&
lmps_map_species_to_unique[j] >= 0) {
setflag[i][j] = 1;
count++;
}
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
return;
@ -406,9 +408,6 @@ void PairKIM::init_style()
if (domain->dimension != 3)
error->all(FLERR,"PairKIM only works with 3D problems");
// set lmps_* bool flags
set_lmps_flags();
int kimerror;
// KIM and Model initialization (only once)
// also sets kim_ind_* and kim_* bool flags
@ -478,6 +477,21 @@ double PairKIM::init_one(int i, int j)
/* ---------------------------------------------------------------------- */
void PairKIM::reinit()
{
// This is called by fix-adapt
// Call parent class implementation
Pair::reinit();
// Then reinit KIM model
int kimerror;
kimerror = pkim->model_reinit();
kim_error(__LINE__,"model_reinit unsuccessful", kimerror);
}
/* ---------------------------------------------------------------------- */
int PairKIM::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
@ -1255,3 +1269,161 @@ void PairKIM::write_descriptor(char** test_descriptor_string)
return;
}
void *PairKIM::extract(const char *str, int &dim)
{
void *paramData;
int kimerror=0;
int ier;
int dummyint;
int isIndexed = 0;
int maxLine = 1024;
int rank;
int validParam = 0;
int numParams;
int *speciesIndex = new int[maxLine];
char *paramStr = new char[maxLine];
char *paramName;
char *indexStr;
char message[maxLine];
int offset;
double* paramPtr;
// set dim to 0, we will always deal with scalars to circumvent lammps species
// indexing
dim = 0;
// copy the input str into paramStr for parsing
strcpy(paramStr, str);
// get the name of the parameter (whatever is before ":")
paramName = strtok(paramStr, ":");
if (0 == strcmp(paramName, str))
paramName = (char*) str;
else
isIndexed = 1;
// parse the rest of the string into tokens deliminated by "," and convert
// them to integers, saving them into speciesIndex
int count = -1;
if (isIndexed == 1)
{
while((indexStr = strtok(NULL, ",")) != NULL)
{
count++;
ier = sscanf(indexStr, "%d", &speciesIndex[count]);
if (ier != 1)
{
ier = -1;
break;
}
}
}
if (ier == -1)
{
delete [] speciesIndex, speciesIndex = 0;
delete [] paramStr, paramStr = 0;
kim_error(__LINE__,"error in PairKIM::extract(), invalid parameter-indicie format", KIM_STATUS_FAIL);
}
// check to make sure that the requested parameter is a valid free parameter
kimerror = pkim->get_num_params(&numParams, &dummyint);
kim_error(__LINE__, "get_num_free_params", kimerror);
char **freeParamNames = new char*[numParams];
for (int k = 0; k < numParams; k++)
{
kimerror = pkim->get_free_parameter(k, (const char**) &freeParamNames[k]);
kim_error(__LINE__, "get_free_parameter", kimerror);
if (0 == strcmp(paramName, freeParamNames[k]))
{
validParam = 1;
break;
}
}
delete [] freeParamNames, freeParamNames = 0;
if (validParam == 0)
{
sprintf(message, "Invalid parameter to adapt: \"%s\" is not a FREE_PARAM", paramName);
delete [] speciesIndex, speciesIndex = 0;
delete [] paramStr, paramStr = 0;
kim_error(__LINE__, message, KIM_STATUS_FAIL);
}
// get the parameter arry from pkim object
paramData = pkim->get_data(paramName, &kimerror);
if (kimerror == KIM_STATUS_FAIL)
{
delete [] speciesIndex, speciesIndex = 0;
delete [] paramStr, paramStr = 0;
}
kim_error(__LINE__,"get_data",kimerror);
// get rank and shape of parameter
rank = (*pkim).get_rank(paramName, &kimerror);
if (kimerror == KIM_STATUS_FAIL)
{
delete [] speciesIndex, speciesIndex = 0;
delete [] paramStr, paramStr = 0;
}
kim_error(__LINE__,"get_rank",kimerror);
int *shape = new int[maxLine];
dummyint = (*pkim).get_shape(paramName, shape, &kimerror);
if (kimerror == KIM_STATUS_FAIL)
{
delete [] speciesIndex, speciesIndex = 0;
delete [] paramStr, paramStr = 0;
delete [] shape, shape = 0;
}
kim_error(__LINE__,"get_shape",kimerror);
delete [] paramStr, paramStr = 0;
// check that number of inputs is rank, and that input indicies are less than
// their respective dimensions in shape
if ((count+1) != rank)
{
sprintf(message, "Number of input indicies not equal to rank of specified parameter (%d)", rank);
kimerror = KIM_STATUS_FAIL;
delete [] speciesIndex, speciesIndex = 0;
delete [] shape, shape = 0;
kim_error(__LINE__,message, kimerror);
}
if (isIndexed == 1)
{
for (int i=0; i <= count; i++)
{
if (shape[i] <= speciesIndex[i] || speciesIndex[i] < 0)
{
kimerror = KIM_STATUS_FAIL;
break;
}
}
}
delete [] shape, shape = 0;
if (kimerror == KIM_STATUS_FAIL)
{
sprintf(message, "One or more parameter indicies out of bounds");
delete [] speciesIndex, speciesIndex = 0;
kim_error(__LINE__, message, kimerror);
}
// Cast it to a double
paramPtr = static_cast<double*>(paramData);
// If it is indexed (not just a scalar for the whole model), then get pointer
// corresponding to specified indicies by calculating the adress offset using
// specified indicies and the shape
if (isIndexed == 1)
{
offset = 0;
for (int i = 0; i < (rank-1); i++)
{
offset = (offset + speciesIndex[i]) * shape[i+1];
}
offset = offset + speciesIndex[(rank - 1)];
paramPtr = (paramPtr + offset);
}
delete [] speciesIndex, speciesIndex = 0;
return ((void*) paramPtr);
}