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added LAST option to dump_modify thresh, more restart info printed out to screen

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This commit is contained in:
Steve Plimpton
2016-10-11 12:39:52 -06:00
parent e70d530c46
commit 04f5eadcf1
76 changed files with 494 additions and 276 deletions
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170
src/dump_custom.cpp
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@ -26,6 +26,7 @@
#include "modify.h"
#include "compute.h"
#include "fix.h"
#include "fix_store.h"
#include "memory.h"
#include "error.h"
@ -82,10 +83,17 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
buffer_flag = 1;
iregion = -1;
idregion = NULL;
nthresh = 0;
thresh_array = NULL;
thresh_op = NULL;
thresh_value = NULL;
thresh_last = NULL;
nthreshlast = 0;
thresh_fix = NULL;
thresh_fixID = NULL;
thresh_first = NULL;
// computes, fixes, variables which the dump accesses
@ -193,6 +201,17 @@ DumpCustom::~DumpCustom()
memory->destroy(thresh_array);
memory->destroy(thresh_op);
memory->destroy(thresh_value);
memory->destroy(thresh_last);
// check nfix in case all fixes have already been deleted
for (int i = 0; i < nthreshlast; i++) {
if (modify->nfix) modify->delete_fix(thresh_fixID[i]);
delete [] thresh_fixID[i];
}
memory->sfree(thresh_fix);
memory->sfree(thresh_fixID);
memory->destroy(thresh_first);
for (int i = 0; i < ncompute; i++) delete [] id_compute[i];
memory->sfree(id_compute);
@ -498,9 +517,10 @@ int DumpCustom::count()
// un-choose if any threshold criterion isn't met
if (nthresh) {
double *ptr;
double *ptr,*ptrhold;
double *values;
double value;
int nstride;
int nstride,lastflag;
int nlocal = atom->nlocal;
for (int ithresh = 0; ithresh < nthresh; ithresh++) {
@ -926,32 +946,91 @@ int DumpCustom::count()
}
// unselect atoms that don't meet threshold criterion
// compare to single value or values stored in threshfix
// copy ptr attribute into thresh_fix if this is first comparison
value = thresh_value[ithresh];
if (thresh_last[ithresh] < 0) {
lastflag = 0;
value = thresh_value[ithresh];
} else {
lastflag = 1;
int ilast = thresh_last[ithresh];
values = thresh_fix[ilast]->vstore;
ptrhold = ptr;
if (thresh_first[ilast]) {
thresh_first[ilast] = 0;
for (i = 0; i < nlocal; i++, ptr += nstride) values[i] = *ptr;
ptr = ptrhold;
}
}
if (thresh_op[ithresh] == LT) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr >= value) choose[i] = 0;
if (lastflag) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr >= values[i]) choose[i] = 0;
} else {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr >= value) choose[i] = 0;
}
} else if (thresh_op[ithresh] == LE) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr > value) choose[i] = 0;
if (lastflag) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr > values[i]) choose[i] = 0;
} else {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr > value) choose[i] = 0;
}
} else if (thresh_op[ithresh] == GT) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr <= value) choose[i] = 0;
if (lastflag) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr <= values[i]) choose[i] = 0;
} else {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr <= value) choose[i] = 0;
}
} else if (thresh_op[ithresh] == GE) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr < value) choose[i] = 0;
if (lastflag) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr < values[i]) choose[i] = 0;
} else {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr < value) choose[i] = 0;
}
} else if (thresh_op[ithresh] == EQ) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr != value) choose[i] = 0;
if (lastflag) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr != values[i]) choose[i] = 0;
} else {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr != value) choose[i] = 0;
}
} else if (thresh_op[ithresh] == NEQ) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr == value) choose[i] = 0;
if (lastflag) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr == values[i]) choose[i] = 0;
} else {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && *ptr == value) choose[i] = 0;
}
} else if (thresh_op[ithresh] == XOR) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && (*ptr == 0.0 && value == 0.0) ||
(*ptr != 0.0 && value != 0.0))
choose[i] = 0;
if (lastflag) {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && (*ptr == 0.0 && values[i] == 0.0) ||
(*ptr != 0.0 && values[i] != 0.0))
choose[i] = 0;
} else {
for (i = 0; i < nlocal; i++, ptr += nstride)
if (choose[i] && (*ptr == 0.0 && value == 0.0) ||
(*ptr != 0.0 && value != 0.0))
choose[i] = 0;
}
}
// update values stored in threshfix
if (lastflag) {
ptr = ptrhold;
for (i = 0; i < nlocal; i++, ptr += nstride) values[i] = *ptr;
}
}
}
@ -1594,8 +1673,16 @@ int DumpCustom::modify_param(int narg, char **arg)
thresh_array = NULL;
thresh_op = NULL;
thresh_value = NULL;
thresh_last = NULL;
for (int i = 0; i < nthreshlast; i++) {
modify->delete_fix(thresh_fixID[i]);
delete [] thresh_fixID[i];
}
thresh_fix = NULL;
thresh_fixID = NULL;
thresh_first = NULL;
}
nthresh = 0;
nthresh = nthreshlast = 0;
return 2;
}
@ -1606,7 +1693,8 @@ int DumpCustom::modify_param(int narg, char **arg)
memory->grow(thresh_array,nthresh+1,"dump:thresh_array");
memory->grow(thresh_op,(nthresh+1),"dump:thresh_op");
memory->grow(thresh_value,(nthresh+1),"dump:thresh_value");
memory->grow(thresh_last,(nthresh+1),"dump:thresh_last");
// set attribute type of threshold
// customize by adding to if statement
@ -1830,7 +1918,7 @@ int DumpCustom::modify_param(int narg, char **arg)
field2index[nfield+nthresh] = add_custom(suffix,0);
delete [] suffix;
} else error->all(FLERR,"Invalid dump_modify threshhold operator");
} else error->all(FLERR,"Invalid dump_modify threshold operator");
// set operation type of threshold
@ -1843,9 +1931,43 @@ int DumpCustom::modify_param(int narg, char **arg)
else if (strcmp(arg[2],"|^") == 0) thresh_op[nthresh] = XOR;
else error->all(FLERR,"Invalid dump_modify threshold operator");
// set threshold value
// set threshold value as number or special LAST keyword
// create FixStore to hold LAST values, should work with restart
// id = dump-ID + nthreshlast + DUMP_STORE, fix group = dump group
thresh_value[nthresh] = force->numeric(FLERR,arg[3]);
if (strcmp(arg[3],"LAST") != 0) {
thresh_value[nthresh] = force->numeric(FLERR,arg[3]);
thresh_last[nthresh] = -1;
} else {
thresh_fix = (FixStore **)
memory->srealloc(thresh_fix,(nthreshlast+1)*sizeof(FixStore *),
"dump:thresh_fix");
thresh_fixID = (char **)
memory->srealloc(thresh_fixID,(nthreshlast+1)*sizeof(char *),
"dump:thresh_fixID");
memory->grow(thresh_first,(nthreshlast+1),"dump:thresh_first");
int n = strlen(id) + strlen("_DUMP_STORE") + 8;
thresh_fixID[nthreshlast] = new char[n];
strcpy(thresh_fixID[nthreshlast],id);
sprintf(&thresh_fixID[nthreshlast][strlen(id)],"%d",nthreshlast);
strcat(thresh_fixID[nthreshlast],"_DUMP_STORE");
char **newarg = new char*[6];
newarg[0] = thresh_fixID[nthreshlast];
newarg[1] = group->names[igroup];
newarg[2] = (char *) "STORE";
newarg[3] = (char *) "peratom";
newarg[4] = (char *) "1";
newarg[5] = (char *) "1";
modify->add_fix(6,newarg);
thresh_fix[nthreshlast] = (FixStore *) modify->fix[modify->nfix-1];
delete [] newarg;
thresh_last[nthreshlast] = nthreshlast;
thresh_first[nthreshlast] = 1;
nthreshlast++;
}
nthresh++;
return 4;