merge with current master
This commit is contained in:
Steve Plimpton
@ -1,6 +1,6 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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https://lammps.sandia.gov/, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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@ -12,21 +12,18 @@
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------------------------------------------------------------------------- */
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#include "dump_custom.h"
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#include <cstdlib>
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#include <cstring>
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#include <string>
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#include "atom.h"
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#include "force.h"
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#include "domain.h"
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#include "region.h"
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#include "group.h"
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#include "input.h"
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#include "modify.h"
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#include "compute.h"
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#include "domain.h"
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#include "error.h"
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#include "fix.h"
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#include "fix_store.h"
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#include "group.h"
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#include "input.h"
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#include "memory.h"
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#include "error.h"
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#include "modify.h"
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#include "region.h"
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#include "update.h"
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#include "variable.h"
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#include "fmt/format.h"
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@ -56,19 +53,22 @@ enum{LT,LE,GT,GE,EQ,NEQ,XOR};
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DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
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Dump(lmp, narg, arg),
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idregion(NULL), thresh_array(NULL), thresh_op(NULL), thresh_value(NULL),
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thresh_last(NULL), thresh_fix(NULL), thresh_fixID(NULL), thresh_first(NULL),
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earg(NULL), vtype(NULL), vformat(NULL), columns(NULL), choose(NULL),
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dchoose(NULL), clist(NULL), field2index(NULL), argindex(NULL), id_compute(NULL),
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compute(NULL), id_fix(NULL), fix(NULL), id_variable(NULL), variable(NULL),
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vbuf(NULL), id_custom(NULL), custom(NULL), custom_flag(NULL), typenames(NULL),
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pack_choice(NULL)
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idregion(nullptr), thresh_array(nullptr), thresh_op(nullptr), thresh_value(nullptr),
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thresh_last(nullptr), thresh_fix(nullptr),
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thresh_fixID(nullptr), thresh_first(nullptr),
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earg(nullptr), vtype(nullptr), vformat(nullptr), columns(nullptr), choose(nullptr),
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dchoose(nullptr), clist(nullptr), field2index(nullptr),
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argindex(nullptr), id_compute(nullptr),
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compute(nullptr), id_fix(nullptr), fix(nullptr),
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id_variable(nullptr), variable(nullptr),
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vbuf(nullptr), id_custom(nullptr), custom(nullptr), custom_flag(nullptr),
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typenames(nullptr), pack_choice(nullptr)
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{
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if (narg == 5) error->all(FLERR,"No dump custom arguments specified");
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clearstep = 1;
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nevery = force->inumeric(FLERR,arg[3]);
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nevery = utils::inumeric(FLERR,arg[3],false,lmp);
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if (nevery <= 0) error->all(FLERR,"Illegal dump custom command");
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// expand args if any have wildcard character "*"
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@ -77,7 +77,7 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
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// nfield may be shrunk below if extra optional args exist
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expand = 0;
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nfield = nargnew = input->expand_args(narg-5,&arg[5],1,earg);
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nfield = nargnew = utils::expand_args(FLERR,narg-5,&arg[5],1,earg,lmp);
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if (earg != &arg[5]) expand = 1;
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// allocate field vectors
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@ -90,38 +90,38 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
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buffer_allow = 1;
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buffer_flag = 1;
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iregion = -1;
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idregion = NULL;
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idregion = nullptr;
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nthresh = 0;
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thresh_array = NULL;
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thresh_op = NULL;
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thresh_value = NULL;
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thresh_last = NULL;
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thresh_array = nullptr;
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thresh_op = nullptr;
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thresh_value = nullptr;
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thresh_last = nullptr;
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nthreshlast = 0;
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thresh_fix = NULL;
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thresh_fixID = NULL;
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thresh_first = NULL;
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thresh_fix = nullptr;
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thresh_fixID = nullptr;
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thresh_first = nullptr;
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// computes, fixes, variables which the dump accesses
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ncompute = 0;
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id_compute = NULL;
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compute = NULL;
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id_compute = nullptr;
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compute = nullptr;
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nfix = 0;
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id_fix = NULL;
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fix = NULL;
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id_fix = nullptr;
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fix = nullptr;
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nvariable = 0;
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id_variable = NULL;
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variable = NULL;
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vbuf = NULL;
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id_variable = nullptr;
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variable = nullptr;
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vbuf = nullptr;
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ncustom = 0;
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id_custom = NULL;
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custom = NULL;
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custom_flag = NULL;
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id_custom = nullptr;
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custom = nullptr;
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custom_flag = nullptr;
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// process attributes
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// ioptional = start of additional optional args in expanded args
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@ -146,9 +146,9 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
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// atom selection arrays
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maxlocal = 0;
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choose = NULL;
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dchoose = NULL;
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clist = NULL;
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choose = nullptr;
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dchoose = nullptr;
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clist = nullptr;
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// default element name for all types = C
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@ -161,21 +161,21 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
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// setup format strings
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vformat = new char*[size_one];
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vformat = new char*[nfield];
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format_default = new char[4*size_one+1];
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format_default = new char[4*nfield+1];
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format_default[0] = '\0';
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for (int i = 0; i < size_one; i++) {
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for (int i = 0; i < nfield; i++) {
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if (vtype[i] == Dump::INT) strcat(format_default,"%d ");
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else if (vtype[i] == Dump::DOUBLE) strcat(format_default,"%g ");
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else if (vtype[i] == Dump::STRING) strcat(format_default,"%s ");
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else if (vtype[i] == Dump::BIGINT) strcat(format_default,BIGINT_FORMAT " ");
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vformat[i] = NULL;
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vformat[i] = nullptr;
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}
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format_column_user = new char*[size_one];
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for (int i = 0; i < size_one; i++) format_column_user[i] = NULL;
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format_column_user = new char*[nfield];
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for (int i = 0; i < nfield; i++) format_column_user[i] = nullptr;
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// setup column string
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@ -249,12 +249,12 @@ DumpCustom::~DumpCustom()
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delete [] typenames;
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if (vformat) {
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for (int i = 0; i < size_one; i++) delete [] vformat[i];
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for (int i = 0; i < nfield; i++) delete [] vformat[i];
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delete [] vformat;
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}
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if (format_column_user) {
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for (int i = 0; i < size_one; i++) delete [] format_column_user[i];
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for (int i = 0; i < nfield; i++) delete [] format_column_user[i];
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delete [] format_column_user;
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}
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@ -282,10 +282,10 @@ void DumpCustom::init_style()
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// lo priority = line, medium priority = int/float, hi priority = column
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char *ptr;
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for (int i = 0; i < size_one; i++) {
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for (int i = 0; i < nfield; i++) {
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if (i == 0) ptr = strtok(format," \0");
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else ptr = strtok(NULL," \0");
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if (ptr == NULL) error->all(FLERR,"Dump_modify format line is too short");
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else ptr = strtok(nullptr," \0");
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if (ptr == nullptr) error->all(FLERR,"Dump_modify format line is too short");
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delete [] vformat[i];
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if (format_column_user[i]) {
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@ -305,7 +305,7 @@ void DumpCustom::init_style()
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strcpy(vformat[i],ptr);
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}
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if (i+1 < size_one) vformat[i] = strcat(vformat[i]," ");
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if (i+1 < nfield) vformat[i] = strcat(vformat[i]," ");
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}
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// setup boundary string
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@ -477,7 +477,7 @@ void DumpCustom::header_binary(bigint ndump)
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fwrite(&boxyhi,sizeof(double),1,fp);
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fwrite(&boxzlo,sizeof(double),1,fp);
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fwrite(&boxzhi,sizeof(double),1,fp);
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fwrite(&size_one,sizeof(int),1,fp);
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fwrite(&nfield,sizeof(int),1,fp);
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header_unit_style_binary();
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header_time_binary();
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@ -506,7 +506,7 @@ void DumpCustom::header_binary_triclinic(bigint ndump)
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fwrite(&boxxy,sizeof(double),1,fp);
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fwrite(&boxxz,sizeof(double),1,fp);
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fwrite(&boxyz,sizeof(double),1,fp);
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fwrite(&size_one,sizeof(int),1,fp);
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fwrite(&nfield,sizeof(int),1,fp);
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header_unit_style_binary();
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header_time_binary();
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@ -1203,13 +1203,13 @@ int DumpCustom::convert_string(int n, double *mybuf)
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int offset = 0;
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int m = 0;
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for (i = 0; i < n; i++) {
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if (offset + size_one*ONEFIELD > maxsbuf) {
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if (offset + nfield*ONEFIELD > maxsbuf) {
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if ((bigint) maxsbuf + DELTA > MAXSMALLINT) return -1;
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maxsbuf += DELTA;
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memory->grow(sbuf,maxsbuf,"dump:sbuf");
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}
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for (j = 0; j < size_one; j++) {
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for (j = 0; j < nfield; j++) {
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if (vtype[j] == Dump::INT)
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offset += sprintf(&sbuf[offset],vformat[j],static_cast<int> (mybuf[m]));
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else if (vtype[j] == Dump::DOUBLE)
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@ -1258,7 +1258,7 @@ void DumpCustom::write_lines(int n, double *mybuf)
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int m = 0;
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for (i = 0; i < n; i++) {
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for (j = 0; j < size_one; j++) {
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for (j = 0; j < nfield; j++) {
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if (vtype[j] == Dump::INT) fprintf(fp,vformat[j],static_cast<int> (mybuf[m]));
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else if (vtype[j] == Dump::DOUBLE) fprintf(fp,vformat[j],mybuf[m]);
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else if (vtype[j] == Dump::STRING)
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@ -1693,7 +1693,7 @@ int DumpCustom::add_variable(char *id)
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variable = new int[nvariable+1];
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delete [] vbuf;
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vbuf = new double*[nvariable+1];
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for (int i = 0; i <= nvariable; i++) vbuf[i] = NULL;
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for (int i = 0; i <= nvariable; i++) vbuf[i] = nullptr;
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int n = strlen(id) + 1;
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id_variable[nvariable] = new char[n];
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@ -1755,9 +1755,9 @@ int DumpCustom::modify_param(int narg, char **arg)
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if (strcmp(arg[1],"none") == 0) {
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// just clear format_column_user allocated by this dump child class
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for (int i = 0; i < size_one; i++) {
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for (int i = 0; i < nfield; i++) {
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delete [] format_column_user[i];
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format_column_user[i] = NULL;
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format_column_user[i] = nullptr;
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}
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return 2;
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}
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@ -1775,7 +1775,7 @@ int DumpCustom::modify_param(int narg, char **arg)
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// replace "d" in format_int_user with bigint format specifier
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// use of &str[1] removes leading '%' from BIGINT_FORMAT string
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char *ptr = strchr(format_int_user,'d');
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if (ptr == NULL)
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if (ptr == nullptr)
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error->all(FLERR,
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"Dump_modify int format does not contain d character");
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char str[8];
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@ -1791,8 +1791,8 @@ int DumpCustom::modify_param(int narg, char **arg)
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strcpy(format_float_user,arg[2]);
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} else {
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int i = force->inumeric(FLERR,arg[1]) - 1;
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if (i < 0 || i >= size_one)
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int i = utils::inumeric(FLERR,arg[1],false,lmp) - 1;
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if (i < 0 || i >= nfield)
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error->all(FLERR,"Illegal dump_modify command");
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if (format_column_user[i]) delete [] format_column_user[i];
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int n = strlen(arg[2]) + 1;
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@ -1837,17 +1837,17 @@ int DumpCustom::modify_param(int narg, char **arg)
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memory->destroy(thresh_array);
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memory->destroy(thresh_op);
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memory->destroy(thresh_value);
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thresh_array = NULL;
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thresh_op = NULL;
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thresh_value = NULL;
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thresh_last = NULL;
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thresh_array = nullptr;
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thresh_op = nullptr;
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thresh_value = nullptr;
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thresh_last = nullptr;
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for (int i = 0; i < nthreshlast; i++) {
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modify->delete_fix(thresh_fixID[i]);
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delete [] thresh_fixID[i];
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}
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thresh_fix = NULL;
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thresh_fixID = NULL;
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thresh_first = NULL;
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thresh_fix = nullptr;
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thresh_fixID = nullptr;
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thresh_first = nullptr;
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}
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nthresh = nthreshlast = 0;
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return 2;
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@ -2127,7 +2127,7 @@ int DumpCustom::modify_param(int narg, char **arg)
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// id = dump-ID + nthreshlast + DUMP_STORE, fix group = dump group
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if (strcmp(arg[3],"LAST") != 0) {
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thresh_value[nthresh] = force->numeric(FLERR,arg[3]);
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thresh_value[nthresh] = utils::numeric(FLERR,arg[3],false,lmp);
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thresh_last[nthresh] = -1;
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} else {
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thresh_fix = (FixStore **)
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@ -2161,9 +2161,9 @@ int DumpCustom::modify_param(int narg, char **arg)
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return # of bytes of allocated memory in buf, choose, variable arrays
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------------------------------------------------------------------------- */
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bigint DumpCustom::memory_usage()
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double DumpCustom::memory_usage()
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{
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bigint bytes = Dump::memory_usage();
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double bytes = Dump::memory_usage();
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bytes += memory->usage(choose,maxlocal);
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bytes += memory->usage(dchoose,maxlocal);
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bytes += memory->usage(clist,maxlocal);
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