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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1257 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2007-12-13 18:16:04 +00:00
parent f07b480280
commit 22a477c3d2
4 changed files with 242 additions and 90 deletions
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302
src/dump_custom.cpp
View File

@ -19,6 +19,8 @@
#include "domain.h"
#include "region.h"
#include "group.h"
#include "input.h"
#include "variable.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
@ -34,7 +36,7 @@ enum{TAG,MOL,TYPE,X,Y,Z,XS,YS,ZS,XU,YU,ZU,IX,IY,IZ,
VX,VY,VZ,FX,FY,FZ,
Q,MUX,MUY,MUZ,
QUATW,QUATI,QUATJ,QUATK,TQX,TQY,TQZ,
COMPUTE,FIX};
COMPUTE,FIX,VARIABLE};
enum{LT,LE,GT,GE,EQ,NEQ};
enum{INT,DOUBLE};
@ -57,20 +59,23 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
thresh_op = NULL;
thresh_value = NULL;
// compute and fix objects dump may create
// compute, fix, variables the dump accesses
field2index = (int *) memory->smalloc(nfield*sizeof(int),"dump:field2index");
argindex = (int *) memory->smalloc(nfield*sizeof(int),"dump:argindex");
ncompute = 0;
id_compute = NULL;
compute = NULL;
field2compute = (int *) memory->smalloc(nfield*sizeof(int),
"dump:field2compute");
arg_compute = (int *) memory->smalloc(nfield*sizeof(int),"dump:arg_compute");
nfix = 0;
id_fix = NULL;
fix = NULL;
field2fix = (int *) memory->smalloc(nfield*sizeof(int),"dump:field2fix");
arg_fix = (int *) memory->smalloc(nfield*sizeof(int),"dump:arg_fix");
nvariable = 0;
id_variable = NULL;
variable = NULL;
vbuf = NULL;
// process keywords
@ -111,20 +116,25 @@ DumpCustom::~DumpCustom()
memory->sfree(thresh_op);
memory->sfree(thresh_value);
memory->sfree(field2index);
memory->sfree(argindex);
for (int i = 0; i < ncompute; i++) delete [] id_compute[i];
memory->sfree(id_compute);
memory->sfree(compute);
memory->sfree(field2compute);
memory->sfree(arg_compute);
delete [] compute;
for (int i = 0; i < nfix; i++) delete [] id_fix[i];
memory->sfree(id_fix);
memory->sfree(fix);
memory->sfree(field2fix);
memory->sfree(arg_fix);
delete [] fix;
delete [] choose;
delete [] dchoose;
for (int i = 0; i < nvariable; i++) delete [] id_variable[i];
memory->sfree(id_variable);
delete [] variable;
for (int i = 0; i < nvariable; i++) memory->sfree(vbuf[i]);
delete [] vbuf;
memory->sfree(choose);
memory->sfree(dchoose);
for (int i = 0; i < size_one; i++) delete [] vformat[i];
delete [] vformat;
@ -163,7 +173,7 @@ void DumpCustom::init()
if (binary) write_choice = &DumpCustom::write_binary;
else write_choice = &DumpCustom::write_text;
// find current ptr for each compute and fix ID
// find current ptr for each compute,fix,variable
// check that fix frequency is acceptable
int icompute;
@ -181,6 +191,13 @@ void DumpCustom::init()
if (nevery % modify->fix[ifix]->peratom_freq)
error->all("Dump custom and fix not computed at compatible times");
}
int ivariable;
for (int i = 0; i < nvariable; i++) {
ivariable = input->variable->find(id_variable[i]);
if (ivariable < 0) error->all("Could not find dump custom variable name");
variable[i] = ivariable;
}
}
/* ---------------------------------------------------------------------- */
@ -230,15 +247,23 @@ int DumpCustom::count()
{
int i;
// grow choose arrays if needed
// grow choose and variable storage arrays if needed
int nlocal = atom->nlocal;
if (nlocal > maxlocal) {
delete [] choose;
delete [] dchoose;
maxlocal = atom->nmax;
choose = new int[maxlocal];
dchoose = new double[maxlocal];
memory->sfree(choose);
memory->sfree(dchoose);
choose = (int *) memory->smalloc(maxlocal*sizeof(int),"dump:choose");
dchoose = (double *)
memory->smalloc(maxlocal*sizeof(double),"dump:dchoose");
for (i = 0; i < nvariable; i++) {
memory->sfree(vbuf[i]);
vbuf[i] = (double *)
memory->smalloc(maxlocal*sizeof(double),"dump:vbuf");
}
}
// invoke Computes for per-atom dump quantities
@ -246,6 +271,18 @@ int DumpCustom::count()
if (ncompute)
for (i = 0; i < ncompute; i++) 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
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();
}
// choose all local atoms for output
for (i = 0; i < nlocal; i++) choose[i] = 1;
@ -430,23 +467,28 @@ int DumpCustom::count()
} else if (thresh_array[ithresh] == COMPUTE) {
i = nfield + ithresh;
if (arg_compute[i] == 0) {
ptr = compute[field2compute[i]]->scalar_atom;
if (argindex[i] == 0) {
ptr = compute[field2index[i]]->scalar_atom;
nstride = 1;
} else {
ptr = &compute[field2compute[i]]->vector_atom[0][arg_compute[i]-1];
nstride = compute[field2compute[i]]->size_peratom;
ptr = &compute[field2index[i]]->vector_atom[0][argindex[i]-1];
nstride = compute[field2index[i]]->size_peratom;
}
} else if (thresh_array[ithresh] == FIX) {
i = nfield + ithresh;
if (arg_fix[i] == 0) {
ptr = fix[field2fix[i]]->scalar_atom;
if (argindex[i] == 0) {
ptr = fix[field2index[i]]->scalar_atom;
nstride = 1;
} else {
ptr = &fix[field2fix[i]]->vector_atom[0][arg_fix[i]-1];
nstride = fix[field2fix[i]]->size_peratom;
ptr = &fix[field2index[i]]->vector_atom[0][argindex[i]-1];
nstride = fix[field2index[i]]->size_peratom;
}
} else if (thresh_array[ithresh] == VARIABLE) {
i = nfield + ithresh;
ptr = vbuf[field2index[i]];
nstride = 1;
}
// unselect atoms that don't meet threshhold criterion
@ -694,25 +736,26 @@ void DumpCustom::parse_fields(int narg, char **arg)
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all("Invalid keyword in dump custom command");
arg_compute[i] = atoi(ptr+1);
argindex[i] = atoi(ptr+1);
*ptr = '\0';
} else arg_compute[i] = 0;
} else argindex[i] = 0;
n = modify->find_compute(suffix);
if (n < 0) error->all("Could not find dump custom compute ID");
if (modify->compute[n]->peratom_flag == 0)
error->all("Dump custom compute ID does not compute peratom info");
if (arg_compute[i] == 0 && modify->compute[n]->size_peratom > 0)
if (argindex[i] == 0 && modify->compute[n]->size_peratom > 0)
error->all("Dump custom compute ID does not compute scalar per atom");
if (arg_compute[i] > 0 && modify->compute[n]->size_peratom == 0)
if (argindex[i] > 0 && modify->compute[n]->size_peratom == 0)
error->all("Dump custom compute ID does not compute vector per atom");
if (arg_compute[i] > 0 &&
arg_compute[i] > modify->compute[n]->size_peratom)
if (argindex[i] > 0 &&
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]);
field2compute[i] = add_compute(suffix);
field2index[i] = add_compute(suffix);
delete [] suffix;
// fix value = f_ID
@ -730,22 +773,43 @@ void DumpCustom::parse_fields(int narg, char **arg)
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all("Invalid keyword in dump custom command");
arg_fix[i] = atoi(ptr+1);
argindex[i] = atoi(ptr+1);
*ptr = '\0';
} else arg_fix[i] = 0;
} else argindex[i] = 0;
n = modify->find_fix(suffix);
if (n < 0) error->all("Could not find dump custom fix ID");
if (modify->fix[n]->peratom_flag == 0)
error->all("Dump custom fix ID does not compute peratom info");
if (arg_fix[i] == 0 && modify->fix[n]->size_peratom > 0)
if (argindex[i] == 0 && modify->fix[n]->size_peratom > 0)
error->all("Dump custom fix ID does not compute scalar per atom");
if (arg_fix[i] > 0 && modify->fix[n]->size_peratom == 0)
if (argindex[i] > 0 && modify->fix[n]->size_peratom == 0)
error->all("Dump custom fix ID does not compute vector per atom");
if (arg_fix[i] > 0 &&
arg_fix[i] > modify->fix[n]->size_peratom)
if (argindex[i] > 0 &&
argindex[i] > modify->fix[n]->size_peratom)
error->all("Dump custom fix ID vector is not large enough");
field2fix[i] = add_fix(suffix);
field2index[i] = add_fix(suffix);
delete [] suffix;
// variable value = v_name
} else if (strncmp(arg[iarg],"v_",2) == 0) {
pack_choice[i] = &DumpCustom::pack_variable;
vtype[i] = DOUBLE;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
strcpy(suffix,&arg[iarg][2]);
argindex[i] = 0;
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");
field2index[i] = add_variable(suffix);
delete [] suffix;
} else error->all("Invalid keyword in dump custom command");
@ -767,8 +831,8 @@ int DumpCustom::add_compute(char *id)
id_compute = (char **)
memory->srealloc(id_compute,(ncompute+1)*sizeof(char *),"dump:id_compute");
compute = (Compute **)
memory->srealloc(compute,(ncompute+1)*sizeof(Compute *),"dump:compute");
delete [] compute;
compute = new Compute*[ncompute+1];
int n = strlen(id) + 1;
id_compute[ncompute] = new char[n];
@ -792,8 +856,8 @@ int DumpCustom::add_fix(char *id)
id_fix = (char **)
memory->srealloc(id_fix,(nfix+1)*sizeof(char *),"dump:id_fix");
fix = (Fix **)
memory->srealloc(fix,(nfix+1)*sizeof(Fix *),"dump:fix");
delete [] fix;
fix = new Fix*[nfix+1];
int n = strlen(id) + 1;
id_fix[nfix] = new char[n];
@ -802,6 +866,35 @@ int DumpCustom::add_fix(char *id)
return nfix-1;
}
/* ----------------------------------------------------------------------
add Variable to list of Variables used by dump
return index of where this Variable is in list
if already in list, do not add, just return index, else add to list
------------------------------------------------------------------------- */
int DumpCustom::add_variable(char *id)
{
int ivariable;
for (ivariable = 0; ivariable < nvariable; ivariable++)
if (strcmp(id,id_variable[ivariable]) == 0) break;
if (ivariable < nvariable) return ivariable;
id_variable = (char **)
memory->srealloc(id_variable,(nvariable+1)*sizeof(char *),
"dump:id_variable");
delete [] variable;
variable = new int[nvariable+1];
delete [] vbuf;
vbuf = new double*[nvariable+1];
for (int i = 0; i <= nvariable; i++) vbuf[i] = NULL;
int n = strlen(id) + 1;
id_variable[nvariable] = new char[n];
strcpy(id_variable[nvariable],id);
nvariable++;
return nvariable-1;
}
/* ---------------------------------------------------------------------- */
int DumpCustom::modify_param(int narg, char **arg)
@ -889,18 +982,17 @@ 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 field2compute and arg_compute arrays,
// since access is beyond nfield
// 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;
field2compute = (int *) memory->srealloc(field2compute,
(nfield+nthresh+1)*sizeof(int),
"dump:field2compute");
arg_compute = (int *) memory->srealloc(arg_compute,
field2index = (int *) memory->srealloc(field2index,
(nfield+nthresh+1)*sizeof(int),
"dump:arg_compute");
"dump:field2index");
argindex = (int *) memory->srealloc(argindex,
(nfield+nthresh+1)*sizeof(int),
"dump:argindex");
int n = strlen(arg[1]);
char *suffix = new char[n];
strcpy(suffix,&arg[1][2]);
@ -909,43 +1001,43 @@ int DumpCustom::modify_param(int narg, char **arg)
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all("Invalid keyword in dump custom command");
arg_compute[nfield+nthresh] = atoi(ptr+1);
argindex[nfield+nthresh] = atoi(ptr+1);
*ptr = '\0';
} else arg_compute[nfield+nthresh] = 0;
} else argindex[nfield+nthresh] = 0;
n = modify->find_compute(suffix);
if (n < 0) error->all("Could not find dump custom compute ID");
if (modify->compute[n]->peratom_flag == 0)
error->all("Dump custom compute ID does not compute peratom info");
if (arg_compute[nfield+nthresh] == 0 &&
if (argindex[nfield+nthresh] == 0 &&
modify->compute[n]->size_peratom > 0)
error->all("Dump custom compute ID does not compute scalar per atom");
if (arg_compute[nfield+nthresh] > 0 &&
if (argindex[nfield+nthresh] > 0 &&
modify->compute[n]->size_peratom == 0)
error->all("Dump custom compute ID does not compute vector per atom");
if (arg_compute[nfield+nthresh] > 0 &&
arg_compute[nfield+nthresh] > modify->compute[n]->size_peratom)
if (argindex[nfield+nthresh] > 0 &&
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]);
field2compute[nfield+nthresh] = add_compute(suffix);
field2index[nfield+nthresh] = add_compute(suffix);
delete [] suffix;
// fix value = f_ID
// if no trailing [], then arg is set to 0, else arg is between []
// must grow field2compute and arg_compute arrays,
// since access is beyond nfield
// must grow field2index and argindex arrays, since access is beyond nfield
} else if (strncmp(arg[1],"f_",2) == 0) {
thresh_array[nthresh] = FIX;
field2fix = (int *) memory->srealloc(field2fix,
(nfield+nthresh+1)*sizeof(int),
"dump:field2fix");
arg_fix = (int *) memory->srealloc(arg_fix,
(nfield+nthresh+1)*sizeof(int),
"dump:arg_fix");
field2index = (int *) memory->srealloc(field2index,
(nfield+nthresh+1)*sizeof(int),
"dump:field2index");
argindex = (int *) memory->srealloc(argindex,
(nfield+nthresh+1)*sizeof(int),
"dump:argindex");
int n = strlen(arg[1]);
char *suffix = new char[n];
strcpy(suffix,&arg[1][2]);
@ -954,25 +1046,51 @@ int DumpCustom::modify_param(int narg, char **arg)
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all("Invalid keyword in dump custom command");
arg_fix[nfield+nthresh] = atoi(ptr+1);
argindex[nfield+nthresh] = atoi(ptr+1);
*ptr = '\0';
} else arg_fix[nfield+nthresh] = 0;
} else argindex[nfield+nthresh] = 0;
n = modify->find_fix(suffix);
if (n < 0) error->all("Could not find dump custom fix ID");
if (modify->fix[n]->peratom_flag == 0)
error->all("Dump custom fix ID does not compute peratom info");
if (arg_fix[nfield+nthresh] == 0 &&
if (argindex[nfield+nthresh] == 0 &&
modify->fix[n]->size_peratom > 0)
error->all("Dump custom fix ID does not compute scalar per atom");
if (arg_fix[nfield+nthresh] > 0 &&
if (argindex[nfield+nthresh] > 0 &&
modify->fix[n]->size_peratom == 0)
error->all("Dump custom fix ID does not compute vector per atom");
if (arg_fix[nfield+nthresh] > 0 &&
arg_fix[nfield+nthresh] > modify->fix[n]->size_peratom)
if (argindex[nfield+nthresh] > 0 &&
argindex[nfield+nthresh] > modify->fix[n]->size_peratom)
error->all("Dump custom fix ID vector is not large enough");
field2fix[nfield+nthresh] = add_fix(suffix);
field2index[nfield+nthresh] = add_fix(suffix);
delete [] suffix;
// variable value = v_ID
// must grow field2index and argindex arrays, since access is beyond nfield
} else if (strncmp(arg[1],"v_",2) == 0) {
thresh_array[nthresh] = VARIABLE;
field2index = (int *) memory->srealloc(field2index,
(nfield+nthresh+1)*sizeof(int),
"dump:field2index");
argindex = (int *) memory->srealloc(argindex,
(nfield+nthresh+1)*sizeof(int),
"dump:argindex");
int n = strlen(arg[1]);
char *suffix = new char[n];
strcpy(suffix,&arg[1][2]);
argindex[nfield+nthresh] = 0;
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");
field2index[nfield+nthresh] = add_variable(suffix);
delete [] suffix;
} else error->all("Invalid dump_modify threshhold operator");
@ -999,7 +1117,7 @@ int DumpCustom::modify_param(int narg, char **arg)
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory in buf and choose and local arrays
return # of bytes of allocated memory in buf, choose, variable arrays
------------------------------------------------------------------------- */
double DumpCustom::memory_usage()
@ -1007,6 +1125,7 @@ double DumpCustom::memory_usage()
double bytes = maxbuf * sizeof(double);
bytes += maxlocal * sizeof(int);
bytes += maxlocal * sizeof(double);
bytes += maxlocal * nvariable * sizeof(double);
return bytes;
}
@ -1483,9 +1602,10 @@ void DumpCustom::pack_tqz(int n)
void DumpCustom::pack_compute(int n)
{
double *vector = compute[field2compute[n]]->scalar_atom;
double **array = compute[field2compute[n]]->vector_atom;
int index = arg_compute[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) {
@ -1508,9 +1628,10 @@ void DumpCustom::pack_compute(int n)
void DumpCustom::pack_fix(int n)
{
double *vector = fix[field2fix[n]]->scalar_atom;
double **array = fix[field2fix[n]]->vector_atom;
int index = arg_fix[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) {
@ -1528,3 +1649,18 @@ void DumpCustom::pack_fix(int n)
}
}
}
/* ---------------------------------------------------------------------- */
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;
}
}

19
src/dump_custom.h
View File

@ -37,25 +37,28 @@ class DumpCustom : public Dump {
int *vtype; // type of each vector (INT, DOUBLE)
char **vformat; // format string for each vector element
int maxlocal; // size of choose and local-compute arrays
int maxlocal; // size of atom selection and variable arrays
int *choose; // 1 if output this atom, 0 if no
double *dchoose; // value for each atom to threshhold against
int nfield; // # of keywords listed by user
int *field2index; // which compute,fix,variable calcs this field
int *argindex; // index into compute,fix scalar_atom,vector_atom
// 0 for scalar_atom, 1-N for vector_atom values
int ncompute; // # of Compute objects used by dump
char **id_compute; // their IDs
class Compute **compute; // list of ptrs to the Compute objects
int *field2compute; // which Compute calculates this field
int *arg_compute; // index into Compute scalar_atom,vector_atom
// 0 for scalar_atom, 1-N for vector_atom values
int nfix; // # of Fix objects used by dump
char **id_fix; // their IDs
class Fix **fix; // list of ptrs to the Fix objects
int *field2fix; // which Fix calculates this field
int *arg_fix; // index into Fix scalar_atom,vector_atom
// 0 for scalar_atom, 1-N for vector_atom values
int nvariable; // # of Variables used by dump
char **id_variable; // their names
int *variable; // list of indices for the Variables
double **vbuf; // local storage for variable evaluation
// private methods
@ -67,6 +70,7 @@ class DumpCustom : public Dump {
void parse_fields(int, char **);
int add_compute(char *);
int add_fix(char *);
int add_variable(char *);
int modify_param(int, char **);
typedef void (DumpCustom::*FnPtrHeader)(int);
@ -119,6 +123,7 @@ class DumpCustom : public Dump {
void pack_compute(int);
void pack_fix(int);
void pack_variable(int);
};
}

10
src/variable.cpp
View File

@ -367,6 +367,16 @@ int Variable::find(char *name)
return -1;
}
/* ----------------------------------------------------------------------
return 1 if variable calculates a per-atom quantity, 0 if not
------------------------------------------------------------------------- */
int Variable::peratom(int ivar)
{
if (style[ivar] == ATOM) return 1;
return 0;
}
/* ----------------------------------------------------------------------
remove Nth variable from list and compact list
------------------------------------------------------------------------- */

1
src/variable.h
View File

@ -26,6 +26,7 @@ class Variable : protected Pointers {
void set(char *, char *);
int next(int, char **);
int find(char *);
int peratom(int);
char *retrieve(char *);
void build_parse_tree(int);