From ce5f174281847098dbc36f0eb7d285a6668bd722 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Mon, 1 Aug 2016 20:35:57 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15414
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/dump_cfg.cpp | 75 +++++++++++-------------
src/dump_custom.cpp | 49 ++++++++++++----
src/dump_custom.h | 3 +
src/fix_ave_atom.cpp | 130 +++++++++++++++++++++++------------------
src/fix_ave_time.cpp | 134 +++++++++++++++---------------------------
src/fix_ave_time.h | 2 +-
src/input.cpp | 136 +++++++++++++++++++++++++++++++++++++++++++
src/input.h | 1 +
src/thermo.cpp | 35 +++++++----
9 files changed, 356 insertions(+), 209 deletions(-)
diff --git a/src/dump_cfg.cpp b/src/dump_cfg.cpp
index 9005c3924a..477cdf3b71 100755
--- a/src/dump_cfg.cpp
+++ b/src/dump_cfg.cpp
@@ -46,59 +46,52 @@ DumpCFG::DumpCFG(LAMMPS *lmp, int narg, char **arg) :
{
multifile_override = 0;
- if (narg < 10 ||
- strcmp(arg[5],"mass") != 0 || strcmp(arg[6],"type") != 0 ||
- (strcmp(arg[7],"xs") != 0 && strcmp(arg[7],"xsu") != 0) ||
- (strcmp(arg[8],"ys") != 0 && strcmp(arg[8],"ysu") != 0) ||
- (strcmp(arg[9],"zs") != 0 && strcmp(arg[9],"zsu") != 0))
+ // use earg instead of original arg since it includes expanded wildcards
+ // earg was created by parent DumpCustom
+
+ if (nfield < 5 ||
+ strcmp(earg[0],"mass") != 0 || strcmp(earg[1],"type") != 0 ||
+ (strcmp(earg[2],"xs") != 0 && strcmp(earg[2],"xsu") != 0) ||
+ (strcmp(earg[3],"ys") != 0 && strcmp(earg[3],"ysu") != 0) ||
+ (strcmp(earg[4],"zs") != 0 && strcmp(earg[4],"zsu") != 0))
error->all(FLERR,"Dump cfg arguments must start with "
"'mass type xs ys zs' or 'mass type xsu ysu zsu'");
- if (strcmp(arg[7],"xs") == 0)
- if (strcmp(arg[8],"ysu") == 0 || strcmp(arg[9],"zsu") == 0)
+ if (strcmp(earg[2],"xs") == 0) {
+ if (strcmp(earg[3],"ysu") == 0 || strcmp(earg[4],"zsu") == 0)
error->all(FLERR,
"Dump cfg arguments can not mix xs|ys|zs with xsu|ysu|zsu");
- else unwrapflag = 0;
- else if (strcmp(arg[8],"ys") == 0 || strcmp(arg[9],"zs") == 0)
- error->all(FLERR,
- "Dump cfg arguments can not mix xs|ys|zs with xsu|ysu|zsu");
- else unwrapflag = 1;
+ unwrapflag = 0;
+ } else {
+ if (strcmp(earg[3],"ys") == 0 || strcmp(earg[4],"zs") == 0)
+ error->all(FLERR,
+ "Dump cfg arguments can not mix xs|ys|zs with xsu|ysu|zsu");
+ unwrapflag = 1;
+ }
// setup auxiliary property name strings
- // convert 'X_ID[m]' (X=c,f,v) to 'ID_m'
+ // convert 'X_ID[m]' (X=c,f,v) to 'X_ID_m'
- if (narg > 10) auxname = new char*[narg-10];
+ if (nfield > 5) auxname = new char*[nfield];
else auxname = NULL;
int i = 0;
- for (int iarg = 10; iarg < narg; iarg++, i++) {
- if (strncmp(arg[iarg],"c_",2) == 0 ||
- strncmp(arg[iarg],"f_",2) == 0 ||
- strncmp(arg[iarg],"v_",2) == 0) {
- int n = strlen(arg[iarg]);
- char *suffix = new char[n];
- strcpy(suffix,&arg[iarg][2]);
-
- char *ptr = strchr(suffix,'[');
- if (ptr) {
- if (suffix[strlen(suffix)-1] != ']')
- error->all(FLERR,"Invalid keyword in dump cfg command");
- *ptr = '\0';
- *(ptr+2) = '\0';
- auxname[i] = new char[strlen(suffix) + 3];
- strcpy(auxname[i],suffix);
- strcat(auxname[i],"_");
- strcat(auxname[i],ptr+1);
- } else {
- auxname[i] = new char[strlen(suffix) + 1];
- strcpy(auxname[i],suffix);
- }
-
- delete [] suffix;
+ for (int iarg = 5; iarg < nfield; iarg++, i++) {
+ if ((strncmp(earg[iarg],"c_",2) == 0 ||
+ strncmp(earg[iarg],"f_",2) == 0 ||
+ strncmp(earg[iarg],"v_",2) == 0) && strchr(earg[iarg],'[')) {
+ char *ptr = strchr(earg[iarg],'[');
+ char *ptr2 = strchr(ptr,']');
+ auxname[i] = new char[strlen(earg[iarg])];
+ *ptr = '\0';
+ *ptr2 = '\0';
+ strcpy(auxname[i],earg[iarg]);
+ strcat(auxname[i],"_");
+ strcat(auxname[i],ptr+1);
} else {
- auxname[i] = new char[strlen(arg[iarg]) + 1];
- strcpy(auxname[i],arg[iarg]);
+ auxname[i] = new char[strlen(earg[iarg]) + 1];
+ strcpy(auxname[i],earg[iarg]);
}
}
}
@@ -108,7 +101,7 @@ DumpCFG::DumpCFG(LAMMPS *lmp, int narg, char **arg) :
DumpCFG::~DumpCFG()
{
if (auxname) {
- for (int i = 0; i < nfield-5; i++) delete [] auxname[i];
+ for (int i = 0; i < nfield; i++) delete [] auxname[i];
delete [] auxname;
}
}
diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp
index 1e7356d0a1..d48e6270e4 100644
--- a/src/dump_custom.cpp
+++ b/src/dump_custom.cpp
@@ -62,9 +62,17 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
nevery = force->inumeric(FLERR,arg[3]);
if (nevery <= 0) error->all(FLERR,"Illegal dump custom command");
- // size_one may be shrunk below if additional optional args exist
+ // expand args if any have wildcard character "*"
+ // ok to include trailing optional args,
+ // so long as they do not have "*" between square brackets
+ // nfield may be shrunk below if extra optional args exist
+
+ expand = 0;
+ nfield = input->expand_args(narg-5,&arg[5],1,earg);
+ if (earg != &arg[5]) expand = 1;
+
+ // allocate field vectors
- size_one = nfield = narg - 5;
pack_choice = new FnPtrPack[nfield];
vtype = new int[nfield];
@@ -100,15 +108,24 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
flag_custom = NULL;
// process attributes
- // ioptional = start of additional optional args
- // only dump image and dump movie styles process optional args
+ // ioptional = start of additional optional args in expanded args
- ioptional = parse_fields(narg,arg);
+ ioptional = parse_fields(nfield,earg);
- if (ioptional < narg &&
+ if (ioptional < nfield &&
strcmp(style,"image") != 0 && strcmp(style,"movie") != 0)
error->all(FLERR,"Invalid attribute in dump custom command");
- size_one = nfield = ioptional - 5;
+
+ // noptional = # of optional args
+ // reset nfield to subtract off optional args
+ // reset ioptional to what it would be in original arg list
+ // only dump image and dump movie styles process optional args,
+ // they do not use expanded earg list
+
+ int noptional = nfield - ioptional;
+ nfield -= noptional;
+ size_one = nfield;
+ ioptional = narg - noptional;
// atom selection arrays
@@ -140,11 +157,11 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
// setup column string
int n = 0;
- for (int iarg = 5; iarg < narg; iarg++) n += strlen(arg[iarg]) + 2;
+ for (int iarg = 0; iarg < nfield; iarg++) n += strlen(earg[iarg]) + 2;
columns = new char[n];
columns[0] = '\0';
- for (int iarg = 5; iarg < narg; iarg++) {
- strcat(columns,arg[iarg]);
+ for (int iarg = 0; iarg < nfield; iarg++) {
+ strcat(columns,earg[iarg]);
strcat(columns," ");
}
}
@@ -153,6 +170,14 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
DumpCustom::~DumpCustom()
{
+ // if wildcard expansion occurred, free earg memory from expand_args()
+ // could not do in constructor, b/c some derived classes process earg
+
+ if (expand) {
+ for (int i = 0; i < nfield; i++) delete [] earg[i];
+ memory->sfree(earg);
+ }
+
delete [] pack_choice;
delete [] vtype;
memory->destroy(field2index);
@@ -1018,8 +1043,8 @@ int DumpCustom::parse_fields(int narg, char **arg)
// customize by adding to if statement
int i;
- for (int iarg = 5; iarg < narg; iarg++) {
- i = iarg-5;
+ for (int iarg = 0; iarg < narg; iarg++) {
+ i = iarg;
if (strcmp(arg[iarg],"id") == 0) {
pack_choice[i] = &DumpCustom::pack_id;
diff --git a/src/dump_custom.h b/src/dump_custom.h
index 79e90c1d85..3239a3283f 100644
--- a/src/dump_custom.h
+++ b/src/dump_custom.h
@@ -38,6 +38,9 @@ class DumpCustom : public Dump {
int *thresh_op; // threshhold operation for each nthresh
double *thresh_value; // threshhold value for each nthresh
+ int expand; // flag for whether field args were expanded
+ char **earg; // field names with wildcard expansion
+
int *vtype; // type of each vector (INT, DOUBLE)
char **vformat; // format string for each vector element
diff --git a/src/fix_ave_atom.cpp b/src/fix_ave_atom.cpp
index 96169b7083..9b0375baec 100644
--- a/src/fix_ave_atom.cpp
+++ b/src/fix_ave_atom.cpp
@@ -43,76 +43,92 @@ FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) :
nrepeat = force->inumeric(FLERR,arg[4]);
peratom_freq = force->inumeric(FLERR,arg[5]);
- // parse remaining values
-
- which = new int[narg-6];
- argindex = new int[narg-6];
- ids = new char*[narg-6];
- value2index = new int[narg-6];
- nvalues = 0;
-
- int iarg = 6;
- while (iarg < narg) {
- ids[nvalues] = NULL;
-
- if (strcmp(arg[iarg],"x") == 0) {
- which[nvalues] = X;
- argindex[nvalues++] = 0;
- } else if (strcmp(arg[iarg],"y") == 0) {
- which[nvalues] = X;
- argindex[nvalues++] = 1;
- } else if (strcmp(arg[iarg],"z") == 0) {
- which[nvalues] = X;
- argindex[nvalues++] = 2;
-
- } else if (strcmp(arg[iarg],"vx") == 0) {
- which[nvalues] = V;
- argindex[nvalues++] = 0;
- } else if (strcmp(arg[iarg],"vy") == 0) {
- which[nvalues] = V;
- argindex[nvalues++] = 1;
- } else if (strcmp(arg[iarg],"vz") == 0) {
- which[nvalues] = V;
- argindex[nvalues++] = 2;
-
- } else if (strcmp(arg[iarg],"fx") == 0) {
- which[nvalues] = F;
- argindex[nvalues++] = 0;
- } else if (strcmp(arg[iarg],"fy") == 0) {
- which[nvalues] = F;
- argindex[nvalues++] = 1;
- } else if (strcmp(arg[iarg],"fz") == 0) {
- which[nvalues] = F;
- argindex[nvalues++] = 2;
-
- } else if (strncmp(arg[iarg],"c_",2) == 0 ||
- strncmp(arg[iarg],"f_",2) == 0 ||
- strncmp(arg[iarg],"v_",2) == 0) {
- if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
- else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
- else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
-
- int n = strlen(arg[iarg]);
+ nvalues = narg - 6;
+
+ // expand args if any have wildcard character "*"
+ // this can reset nvalues
+
+ int expand = 0;
+ char **earg,**arghold;
+ nvalues = input->expand_args(nvalues,&arg[6],1,earg);
+
+ if (earg != &arg[6]) expand = 1;
+ arghold = arg;
+ arg = earg;
+
+ // parse values
+
+ which = new int[nvalues];
+ argindex = new int[nvalues];
+ ids = new char*[nvalues];
+ value2index = new int[nvalues];
+
+ for (int i = 0; i < nvalues; i++) {
+ ids[i] = NULL;
+
+ if (strcmp(arg[i],"x") == 0) {
+ which[i] = X;
+ argindex[i++] = 0;
+ } else if (strcmp(arg[i],"y") == 0) {
+ which[i] = X;
+ argindex[i++] = 1;
+ } else if (strcmp(arg[i],"z") == 0) {
+ which[i] = X;
+ argindex[i++] = 2;
+
+ } else if (strcmp(arg[i],"vx") == 0) {
+ which[i] = V;
+ argindex[i++] = 0;
+ } else if (strcmp(arg[i],"vy") == 0) {
+ which[i] = V;
+ argindex[i++] = 1;
+ } else if (strcmp(arg[i],"vz") == 0) {
+ which[i] = V;
+ argindex[i++] = 2;
+
+ } else if (strcmp(arg[i],"fx") == 0) {
+ which[i] = F;
+ argindex[i++] = 0;
+ } else if (strcmp(arg[i],"fy") == 0) {
+ which[i] = F;
+ argindex[i++] = 1;
+ } else if (strcmp(arg[i],"fz") == 0) {
+ which[i] = F;
+ argindex[i++] = 2;
+
+ } else if (strncmp(arg[i],"c_",2) == 0 ||
+ strncmp(arg[i],"f_",2) == 0 ||
+ strncmp(arg[i],"v_",2) == 0) {
+ if (arg[i][0] == 'c') which[i] = COMPUTE;
+ else if (arg[i][0] == 'f') which[i] = FIX;
+ else if (arg[i][0] == 'v') which[i] = VARIABLE;
+
+ int n = strlen(arg[i]);
char *suffix = new char[n];
- strcpy(suffix,&arg[iarg][2]);
+ strcpy(suffix,&arg[i][2]);
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all(FLERR,"Illegal fix ave/atom command");
- argindex[nvalues] = atoi(ptr+1);
+ argindex[i] = atoi(ptr+1);
*ptr = '\0';
- } else argindex[nvalues] = 0;
+ } else argindex[i] = 0;
n = strlen(suffix) + 1;
- ids[nvalues] = new char[n];
- strcpy(ids[nvalues],suffix);
- nvalues++;
+ ids[i] = new char[n];
+ strcpy(ids[i],suffix);
delete [] suffix;
} else error->all(FLERR,"Illegal fix ave/atom command");
+ }
+
+ // if wildcard expansion occurred, free earg memory from exapnd_args()
- iarg++;
+ if (expand) {
+ for (int i = 0; i < nvalues; i++) delete [] earg[i];
+ memory->sfree(earg);
+ arg = arghold;
}
// setup and error check
diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp
index 588aca4738..56a3900f0e 100644
--- a/src/fix_ave_time.cpp
+++ b/src/fix_ave_time.cpp
@@ -73,89 +73,46 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
if (nvalues == 0) error->all(FLERR,"No values in fix ave/time command");
- options(narg,arg);
+ options(iarg,narg,arg);
- // parse values until one isn't recognized
- // if mode = VECTOR and value is a global array:
- // expand it as if columns listed one by one
- // adjust nvalues accordingly via maxvalues
+ // expand args if any have wildcard character "*"
+ // this can reset nvalues
- which = argindex = value2index = offcol = varlen = NULL;
- ids = NULL;
- int maxvalues = nvalues;
- allocate_values(maxvalues);
- nvalues = 0;
+ int expand = 0;
+ char **earg,**arghold;
+ nvalues = input->expand_args(nvalues,&arg[6],mode,earg);
- iarg = 6;
- while (iarg < narg) {
- if (strncmp(arg[iarg],"c_",2) == 0 ||
- strncmp(arg[iarg],"f_",2) == 0 ||
- strncmp(arg[iarg],"v_",2) == 0) {
- if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
- else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
- else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
-
- int n = strlen(arg[iarg]);
- char *suffix = new char[n];
- strcpy(suffix,&arg[iarg][2]);
-
- char *ptr = strchr(suffix,'[');
- if (ptr) {
- if (suffix[strlen(suffix)-1] != ']')
- error->all(FLERR,"Illegal fix ave/time command");
- argindex[nvalues] = atoi(ptr+1);
- *ptr = '\0';
- } else argindex[nvalues] = 0;
-
- n = strlen(suffix) + 1;
- ids[nvalues] = new char[n];
- strcpy(ids[nvalues],suffix);
- delete [] suffix;
-
- if (mode == VECTOR && which[nvalues] == COMPUTE &&
- argindex[nvalues] == 0) {
- int icompute = modify->find_compute(ids[nvalues]);
- if (icompute < 0)
- error->all(FLERR,"Compute ID for fix ave/time does not exist");
- if (modify->compute[icompute]->array_flag) {
- int ncols = modify->compute[icompute]->size_array_cols;
- maxvalues += ncols-1;
- allocate_values(maxvalues);
- argindex[nvalues] = 1;
- for (int icol = 1; icol < ncols; icol++) {
- which[nvalues+icol] = which[nvalues];
- argindex[nvalues+icol] = icol+1;
- n = strlen(ids[nvalues]) + 1;
- ids[nvalues+icol] = new char[n];
- strcpy(ids[nvalues+icol],ids[nvalues]);
- }
- nvalues += ncols-1;
- }
+ if (earg != &arg[6]) expand = 1;
+ arghold = arg;
+ arg = earg;
- } else if (mode == VECTOR && which[nvalues] == FIX &&
- argindex[nvalues] == 0) {
- int ifix = modify->find_fix(ids[nvalues]);
- if (ifix < 0)
- error->all(FLERR,"Fix ID for fix ave/time does not exist");
- if (modify->fix[ifix]->array_flag) {
- int ncols = modify->fix[ifix]->size_array_cols;
- maxvalues += ncols-1;
- allocate_values(maxvalues);
- argindex[nvalues] = 1;
- for (int icol = 1; icol < ncols; icol++) {
- which[nvalues+icol] = which[nvalues];
- argindex[nvalues+icol] = icol+1;
- n = strlen(ids[nvalues]) + 1;
- ids[nvalues+icol] = new char[n];
- strcpy(ids[nvalues+icol],ids[nvalues]);
- }
- nvalues += ncols-1;
- }
- }
+ // parse values
- nvalues++;
- iarg++;
- } else break;
+ which = argindex = value2index = offcol = varlen = NULL;
+ ids = NULL;
+ allocate_values(nvalues);
+
+ for (int i = 0; i < nvalues; i++) {
+ if (arg[i][0] == 'c') which[i] = COMPUTE;
+ else if (arg[i][0] == 'f') which[i] = FIX;
+ else if (arg[i][0] == 'v') which[i] = VARIABLE;
+
+ int n = strlen(arg[i]);
+ char *suffix = new char[n];
+ strcpy(suffix,&arg[i][2]);
+
+ char *ptr = strchr(suffix,'[');
+ if (ptr) {
+ if (suffix[strlen(suffix)-1] != ']')
+ error->all(FLERR,"Illegal fix ave/time command");
+ argindex[i] = atoi(ptr+1);
+ *ptr = '\0';
+ } else argindex[i] = 0;
+
+ n = strlen(suffix) + 1;
+ ids[i] = new char[n];
+ strcpy(ids[i],suffix);
+ delete [] suffix;
}
// set off columns now that nvalues is finalized
@@ -311,18 +268,13 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
if (title2) fprintf(fp,"%s\n",title2);
else if (mode == SCALAR) {
fprintf(fp,"# TimeStep");
- for (int i = 0; i < nvalues; i++) fprintf(fp," %s",arg[6+i]);
+ for (int i = 0; i < nvalues; i++) fprintf(fp," %s",earg[i]);
fprintf(fp,"\n");
} else fprintf(fp,"# TimeStep Number-of-rows\n");
if (title3 && mode == VECTOR) fprintf(fp,"%s\n",title3);
else if (mode == VECTOR) {
fprintf(fp,"# Row");
- for (int i = 0; i < nvalues; i++) {
- if (which[i] == COMPUTE) fprintf(fp," c_%s",ids[i]);
- else if (which[i] == FIX) fprintf(fp," f_%s",ids[i]);
- else if (which[i] == VARIABLE) fprintf(fp," v_%s",ids[i]);
- if (argindex[i]) fprintf(fp,"[%d]",argindex[i]);
- }
+ for (int i = 0; i < nvalues; i++) fprintf(fp," %s",earg[i]);
fprintf(fp,"\n");
}
if (ferror(fp))
@@ -335,6 +287,15 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
delete [] title2;
delete [] title3;
+ // if wildcard expansion occurred, free earg memory from expand_args()
+ // wait to do this after file comment lines are printed
+
+ if (expand) {
+ for (int i = 0; i < nvalues; i++) delete [] earg[i];
+ memory->sfree(earg);
+ arg = arghold;
+ }
+
// allocate memory for averaging
vector = vector_total = NULL;
@@ -1049,7 +1010,7 @@ double FixAveTime::compute_array(int i, int j)
parse optional args
------------------------------------------------------------------------- */
-void FixAveTime::options(int narg, char **arg)
+void FixAveTime::options(int iarg, int narg, char **arg)
{
// option defaults
@@ -1068,7 +1029,6 @@ void FixAveTime::options(int narg, char **arg)
// optional args
- int iarg = 6 + nvalues;
while (iarg < narg) {
if (strcmp(arg[iarg],"file") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command");
diff --git a/src/fix_ave_time.h b/src/fix_ave_time.h
index 98b665140c..f2f79f1276 100644
--- a/src/fix_ave_time.h
+++ b/src/fix_ave_time.h
@@ -69,7 +69,7 @@ class FixAveTime : public Fix {
int column_length(int);
void invoke_scalar(bigint);
void invoke_vector(bigint);
- void options(int, char **);
+ void options(int, int, char **);
void allocate_values(int);
void allocate_arrays();
bigint nextvalid();
diff --git a/src/input.cpp b/src/input.cpp
index 7983f81532..dda64856dc 100644
--- a/src/input.cpp
+++ b/src/input.cpp
@@ -36,6 +36,7 @@
#include "min.h"
#include "modify.h"
#include "compute.h"
+#include "fix.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
@@ -583,6 +584,141 @@ void Input::substitute(char *&str, char *&str2, int &max, int &max2, int flag)
strcpy(str,str2);
}
+/* ----------------------------------------------------------------------
+ expand arg to earg, for arguments with syntax c_ID[*] or f_ID[*]
+ fields to consider in input arg range from iarg to narg
+ return new expanded # of values, and copy them w/out "*" into earg
+ if any expansion occurs, earg is new allocation, must be freed by caller
+ if no expansion occurs, earg just points to arg, caller need not free
+------------------------------------------------------------------------- */
+
+int Input::expand_args(int narg, char **arg, int mode, char **&earg)
+{
+ int n,iarg,index,nlo,nhi,nmax,which,expandflag,icompute,ifix;
+ char *ptr1,*ptr2,*str;
+
+ ptr1 = NULL;
+ for (iarg = 0; iarg < narg; iarg++) {
+ ptr1 = strchr(arg[iarg],'*');
+ if (ptr1) break;
+ }
+
+ if (!ptr1) {
+ earg = arg;
+ return narg;
+ }
+
+ // maxarg should always end up equal to newarg, so caller can free earg
+
+ int maxarg = narg-iarg;
+ earg = (char **) memory->smalloc(maxarg*sizeof(char *),"input:earg");
+
+ int newarg = 0;
+ for (iarg = 0; iarg < narg; iarg++) {
+ expandflag = 0;
+
+ if (strncmp(arg[iarg],"c_",2) == 0 ||
+ strncmp(arg[iarg],"f_",2) == 0) {
+
+ ptr1 = strchr(&arg[iarg][2],'[');
+ if (ptr1) {
+ ptr2 = strchr(ptr1,']');
+ if (ptr2) {
+ *ptr2 = '\0';
+ if (strchr(ptr1,'*')) {
+ if (arg[iarg][0] == 'c') {
+ *ptr1 = '\0';
+ icompute = modify->find_compute(&arg[iarg][2]);
+ *ptr1 = '[';
+
+ // check for global vector/array, peratom array, local array
+
+ if (icompute >= 0) {
+ if (mode == 0 && modify->compute[icompute]->vector_flag) {
+ nmax = modify->compute[icompute]->size_vector;
+ expandflag = 1;
+ } else if (mode == 1 && modify->compute[icompute]->array_flag) {
+ nmax = modify->compute[icompute]->size_array_cols;
+ expandflag = 1;
+ } else if (modify->compute[icompute]->peratom_flag &&
+ modify->compute[icompute]->size_peratom_cols) {
+ nmax = modify->compute[icompute]->size_peratom_cols;
+ expandflag = 1;
+ } else if (modify->compute[icompute]->local_flag &&
+ modify->compute[icompute]->size_local_cols) {
+ nmax = modify->compute[icompute]->size_local_cols;
+ expandflag = 1;
+ }
+ }
+ } else if (arg[iarg][0] == 'f') {
+ *ptr1 = '\0';
+ ifix = modify->find_fix(&arg[iarg][2]);
+ *ptr1 = '[';
+
+ // check for global vector/array, peratom array, local array
+
+ if (ifix >= 0) {
+ if (mode == 0 && modify->fix[ifix]->vector_flag) {
+ nmax = modify->fix[ifix]->size_vector;
+ expandflag = 1;
+ } else if (mode == 1 && modify->fix[ifix]->array_flag) {
+ nmax = modify->fix[ifix]->size_array_cols;
+ expandflag = 1;
+ } else if (modify->fix[ifix]->peratom_flag &&
+ modify->fix[ifix]->size_peratom_cols) {
+ nmax = modify->fix[ifix]->size_peratom_cols;
+ expandflag = 1;
+ } else if (modify->fix[ifix]->local_flag &&
+ modify->fix[ifix]->size_local_cols) {
+ nmax = modify->fix[ifix]->size_local_cols;
+ expandflag = 1;
+ }
+ }
+ }
+ }
+ *ptr2 = ']';
+ }
+ }
+ }
+
+ if (expandflag) {
+ *ptr2 = '\0';
+ force->bounds(ptr1+1,nmax,nlo,nhi);
+ *ptr2 = ']';
+ if (newarg+nhi-nlo+1 > maxarg) {
+ maxarg += nhi-nlo+1;
+ earg = (char **)
+ memory->srealloc(earg,maxarg*sizeof(char *),"input:earg");
+ }
+ for (index = nlo; index <= nhi; index++) {
+ n = strlen(arg[iarg]) + 16; // 16 = space for large inserted integer
+ str = earg[newarg] = new char[n];
+ strncpy(str,arg[iarg],ptr1+1-arg[iarg]);
+ sprintf(&str[ptr1+1-arg[iarg]],"%d",index);
+ strcat(str,ptr2);
+ newarg++;
+ }
+
+ } else {
+ if (newarg == maxarg) {
+ maxarg++;
+ earg = (char **)
+ memory->srealloc(earg,maxarg*sizeof(char *),"input:earg");
+ }
+ n = strlen(arg[iarg]) + 1;
+ earg[newarg] = new char[n];
+ strcpy(earg[newarg],arg[iarg]);
+ newarg++;
+ }
+ }
+
+ //printf("NEWARG %d\n",newarg);
+ //for (int i = 0; i < newarg; i++)
+ // printf(" arg %d: %s\n",i,earg[i]);
+
+ return newarg;
+}
+
/* ----------------------------------------------------------------------
return number of triple quotes in line
------------------------------------------------------------------------- */
diff --git a/src/input.h b/src/input.h
index ccda3f49b1..c1947fee03 100644
--- a/src/input.h
+++ b/src/input.h
@@ -35,6 +35,7 @@ class Input : protected Pointers {
char *one(const char *); // process a single command
void substitute(char *&, char *&, int &, int &, int);
// substitute for variables in a string
+ int expand_args(int, char **, int, char **&); // expand args due to wildcard
private:
int me; // proc ID
diff --git a/src/thermo.cpp b/src/thermo.cpp
index 5ecc161c8f..1b0fc3c68a 100644
--- a/src/thermo.cpp
+++ b/src/thermo.cpp
@@ -102,7 +102,7 @@ Thermo::Thermo(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
flushflag = 0;
// set style and corresponding lineflag
- // custom style builds its own line of keywords
+ // custom style builds its own line of keywords, including wildcard expansion
// customize a new thermo style by adding to if statement
// allocate line string used for 3 tasks
// concat of custom style args
@@ -121,14 +121,29 @@ Thermo::Thermo(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
} else if (strcmp(style,"custom") == 0) {
if (narg == 1) error->all(FLERR,"Illegal thermo style custom command");
+
+ // expand args if any have wildcard character "*"
+
+ int expand = 0;
+ char **earg;
+ int nvalues = input->expand_args(narg-1,&arg[1],0,earg);
+ if (earg != &arg[1]) expand = 1;
+
line = new char[256+narg*64];
line[0] = '\0';
- for (int iarg = 1; iarg < narg; iarg++) {
- strcat(line,arg[iarg]);
+ for (int iarg = 0; iarg < nvalues; iarg++) {
+ strcat(line,earg[iarg]);
strcat(line," ");
}
line[strlen(line)-1] = '\0';
+ // if wildcard expansion occurred, free earg memory from exapnd_args()
+
+ if (expand) {
+ for (int i = 0; i < nvalues; i++) delete [] earg[i];
+ memory->sfree(earg);
+ }
+
} else error->all(FLERR,"Illegal thermo style command");
// ptrs, flags, IDs for compute objects thermo may use or create
@@ -573,7 +588,7 @@ void Thermo::allocate()
int n = nfield_initial + 1;
keyword = new char*[n];
- for (int i = 0; i < n; i++) keyword[i] = new char[32];
+ for (int i = 0; i < n; i++) keyword[i] = NULL;
vfunc = new FnPtr[n];
vtype = new int[n];
@@ -821,7 +836,6 @@ void Thermo::parse_fields(char *str)
// compute value = c_ID, fix value = f_ID, variable value = v_ID
// count trailing [] and store int arguments
- // copy = at most 8 chars of ID to pass to addfield
} else if ((strncmp(word,"c_",2) == 0) || (strncmp(word,"f_",2) == 0) ||
(strncmp(word,"v_",2) == 0)) {
@@ -829,9 +843,6 @@ void Thermo::parse_fields(char *str)
int n = strlen(word);
char *id = new char[n];
strcpy(id,&word[2]);
- char copy[9];
- strncpy(copy,id,8);
- copy[8] = '\0';
// parse zero or one or two trailing brackets from ID
// argindex1,argindex2 = int inside each bracket pair, 0 if no bracket
@@ -878,7 +889,7 @@ void Thermo::parse_fields(char *str)
field2index[nfield] = add_compute(id,VECTOR);
else
field2index[nfield] = add_compute(id,ARRAY);
- addfield(copy,&Thermo::compute_compute,FLOAT);
+ addfield(word,&Thermo::compute_compute,FLOAT);
} else if (word[0] == 'f') {
n = modify->find_fix(id);
@@ -903,7 +914,7 @@ void Thermo::parse_fields(char *str)
}
field2index[nfield] = add_fix(id);
- addfield(copy,&Thermo::compute_fix,FLOAT);
+ addfield(word,&Thermo::compute_fix,FLOAT);
} else if (word[0] == 'v') {
n = input->variable->find(id);
@@ -919,7 +930,7 @@ void Thermo::parse_fields(char *str)
error->all(FLERR,"Thermo custom variable cannot have two indices");
field2index[nfield] = add_variable(id);
- addfield(copy,&Thermo::compute_variable,FLOAT);
+ addfield(word,&Thermo::compute_variable,FLOAT);
}
delete [] id;
@@ -936,6 +947,8 @@ void Thermo::parse_fields(char *str)
void Thermo::addfield(const char *key, FnPtr func, int typeflag)
{
+ int n = strlen(key) + 1;
+ keyword[nfield] = new char[n];
strcpy(keyword[nfield],key);
vfunc[nfield] = func;
vtype[nfield] = typeflag;
--
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