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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1272 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2008-01-02 19:24:46 +00:00
parent 428ca84042
commit b2e9f7dc10
145 changed files with 2801 additions and 2615 deletions
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185
src/dump_custom.cpp
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@ -40,6 +40,8 @@ enum{TAG,MOL,TYPE,X,Y,Z,XS,YS,ZS,XU,YU,ZU,IX,IY,IZ,
enum{LT,LE,GT,GE,EQ,NEQ};
enum{INT,DOUBLE};
#define INVOKED_PERATOM 4 // same as in computes
/* ---------------------------------------------------------------------- */
DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
@ -247,7 +249,7 @@ int DumpCustom::count()
{
int i;
// grow choose and variable storage arrays if needed
// grow choose and variable vbuf arrays if needed
int nlocal = atom->nlocal;
if (nlocal > maxlocal) {
@ -267,22 +269,19 @@ int DumpCustom::count()
}
// invoke Computes for per-atom dump quantities
// only if not already invoked
if (ncompute)
for (i = 0; i < ncompute; i++) compute[i]->compute_peratom();
for (i = 0; i < ncompute; i++)
if (!(compute[i]->invoked & INVOKED_PERATOM))
compute[i]->compute_peratom();
// invoke Variables for per-atom dump quantities
// parse variable once to create parse tree
// evaluate tree for all atoms, will be zero for atoms not in group
// free parse tree memory stored by Variable
// evaluate atom-style Variables for per-atom dump quantities
if (nvariable)
for (i = 0; i < nvariable; i++) {
input->variable->build_parse_tree(variable[i]);
input->variable->evaluate_parse_tree(igroup,vbuf[i]);
input->variable->free_parse_tree();
}
for (i = 0; i < nvariable; i++)
input->variable->compute_atom(variable[i],igroup,vbuf[i],1,0);
// choose all local atoms for output
for (i = 0; i < nlocal; i++) choose[i] = 1;
@ -722,7 +721,6 @@ void DumpCustom::parse_fields(int narg, char **arg)
// compute value = c_ID
// if no trailing [], then arg is set to 0, else arg is between []
// if Compute has pre-computes, first add them to list
} else if (strncmp(arg[iarg],"c_",2) == 0) {
pack_choice[i] = &DumpCustom::pack_compute;
@ -752,9 +750,6 @@ void DumpCustom::parse_fields(int narg, char **arg)
argindex[i] > modify->compute[n]->size_peratom)
error->all("Dump custom compute ID vector is not large enough");
if (modify->compute[n]->npre)
for (int ic = 0; ic < modify->compute[n]->npre; ic++)
int tmp = add_compute(modify->compute[n]->id_pre[ic]);
field2index[i] = add_compute(suffix);
delete [] suffix;
@ -806,8 +801,8 @@ void DumpCustom::parse_fields(int narg, char **arg)
n = input->variable->find(suffix);
if (n < 0) error->all("Could not find dump custom variable name");
if (input->variable->peratom(n) == 0)
error->all("Dump custom variable does not compute peratom info");
if (input->variable->atomstyle(n) == 0)
error->all("Dump custom variable is not atom-style variable");
field2index[i] = add_variable(suffix);
delete [] suffix;
@ -983,7 +978,6 @@ int DumpCustom::modify_param(int narg, char **arg)
// compute value = c_ID
// if no trailing [], then arg is set to 0, else arg is between []
// must grow field2index and argindex arrays, since access is beyond nfield
// if Compute has pre-computes, first add them to list
else if (strncmp(arg[1],"c_",2) == 0) {
thresh_array[nthresh] = COMPUTE;
@ -1020,9 +1014,6 @@ int DumpCustom::modify_param(int narg, char **arg)
argindex[nfield+nthresh] > modify->compute[n]->size_peratom)
error->all("Dump custom compute ID vector is not large enough");
if (modify->compute[n]->npre)
for (int ic = 0; ic < modify->compute[n]->npre; ic++)
int tmp = add_compute(modify->compute[n]->id_pre[ic]);
field2index[nfield+nthresh] = add_compute(suffix);
delete [] suffix;
@ -1087,8 +1078,8 @@ int DumpCustom::modify_param(int narg, char **arg)
n = input->variable->find(suffix);
if (n < 0) error->all("Could not find dump custom variable name");
if (input->variable->peratom(n) == 0)
error->all("Dump custom variable does not compute peratom info");
if (input->variable->atomstyle(n) == 0)
error->all("Dump custom variable is not atom-style variable");
field2index[nfield+nthresh] = add_variable(suffix);
delete [] suffix;
@ -1129,11 +1120,80 @@ double DumpCustom::memory_usage()
return bytes;
}
// ----------------------------------------------------------------------
// one method for every keyword dump custom can output
// the atom quantity is packed into buf starting at n with stride size_one
// customize by adding a method
// ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
extraction of Compute, Fix, Variable results
------------------------------------------------------------------------- */
void DumpCustom::pack_compute(int n)
{
double *vector = compute[field2index[n]]->scalar_atom;
double **array = compute[field2index[n]]->vector_atom;
int index = argindex[n];
int nlocal = atom->nlocal;
if (index == 0) {
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = vector[i];
n += size_one;
}
} else {
index--;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = array[i][index];
n += size_one;
}
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_fix(int n)
{
double *vector = fix[field2index[n]]->scalar_atom;
double **array = fix[field2index[n]]->vector_atom;
int index = argindex[n];
int nlocal = atom->nlocal;
if (index == 0) {
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = vector[i];
n += size_one;
}
} else {
index--;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = array[i][index];
n += size_one;
}
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_variable(int n)
{
double *vector = vbuf[field2index[n]];
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = vector[i];
n += size_one;
}
}
/* ----------------------------------------------------------------------
one method for every keyword dump custom can output
the atom quantity is packed into buf starting at n with stride size_one
customize a new keyword by adding a method
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
@ -1597,70 +1657,3 @@ void DumpCustom::pack_tqz(int n)
n += size_one;
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_compute(int n)
{
double *vector = compute[field2index[n]]->scalar_atom;
double **array = compute[field2index[n]]->vector_atom;
int index = argindex[n];
int nlocal = atom->nlocal;
if (index == 0) {
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = vector[i];
n += size_one;
}
} else {
index--;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = array[i][index];
n += size_one;
}
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_fix(int n)
{
double *vector = fix[field2index[n]]->scalar_atom;
double **array = fix[field2index[n]]->vector_atom;
int index = argindex[n];
int nlocal = atom->nlocal;
if (index == 0) {
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = vector[i];
n += size_one;
}
} else {
index--;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = array[i][index];
n += size_one;
}
}
}
/* ---------------------------------------------------------------------- */
void DumpCustom::pack_variable(int n)
{
double *vector = vbuf[field2index[n]];
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (choose[i]) {
buf[n] = vector[i];
n += size_one;
}
}