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Merge from lammps master

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This commit is contained in:
julient31
2018-05-21 16:06:53 -06:00
parent 437e854741 94c6d2d546
commit 1641f78e3e
1621 changed files with 28923 additions and 7380 deletions
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144
src/dump_custom.cpp
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@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include <cmath>
#include <cstdlib>
#include <cstring>
#include "dump_custom.h"
#include "atom.h"
#include "force.h"
@ -46,7 +46,6 @@ enum{ID,MOL,PROC,PROCP1,TYPE,ELEMENT,MASS,
TQX,TQY,TQZ,
COMPUTE,FIX,VARIABLE,INAME,DNAME};
enum{LT,LE,GT,GE,EQ,NEQ,XOR};
enum{INT,DOUBLE,STRING,BIGINT}; // same as in DumpCFG
#define INVOKED_PERATOM 8
#define ONEFIELD 32
@ -61,7 +60,7 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
earg(NULL), vtype(NULL), vformat(NULL), columns(NULL), choose(NULL),
dchoose(NULL), clist(NULL), field2index(NULL), argindex(NULL), id_compute(NULL),
compute(NULL), id_fix(NULL), fix(NULL), id_variable(NULL), variable(NULL),
vbuf(NULL), id_custom(NULL), flag_custom(NULL), typenames(NULL),
vbuf(NULL), id_custom(NULL), flag_custom(NULL), typenames(NULL),
pack_choice(NULL)
{
if (narg == 5) error->all(FLERR,"No dump custom arguments specified");
@ -166,10 +165,10 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
format_default[0] = '\0';
for (int i = 0; i < size_one; i++) {
if (vtype[i] == INT) strcat(format_default,"%d ");
else if (vtype[i] == DOUBLE) strcat(format_default,"%g ");
else if (vtype[i] == STRING) strcat(format_default,"%s ");
else if (vtype[i] == BIGINT) strcat(format_default,BIGINT_FORMAT " ");
if (vtype[i] == Dump::INT) strcat(format_default,"%d ");
else if (vtype[i] == Dump::DOUBLE) strcat(format_default,"%g ");
else if (vtype[i] == Dump::STRING) strcat(format_default,"%s ");
else if (vtype[i] == Dump::BIGINT) strcat(format_default,BIGINT_FORMAT " ");
vformat[i] = NULL;
}
@ -285,13 +284,13 @@ void DumpCustom::init_style()
if (format_column_user[i]) {
vformat[i] = new char[strlen(format_column_user[i]) + 2];
strcpy(vformat[i],format_column_user[i]);
} else if (vtype[i] == INT && format_int_user) {
} else if (vtype[i] == Dump::INT && format_int_user) {
vformat[i] = new char[strlen(format_int_user) + 2];
strcpy(vformat[i],format_int_user);
} else if (vtype[i] == DOUBLE && format_float_user) {
} else if (vtype[i] == Dump::DOUBLE && format_float_user) {
vformat[i] = new char[strlen(format_float_user) + 2];
strcpy(vformat[i],format_float_user);
} else if (vtype[i] == BIGINT && format_bigint_user) {
} else if (vtype[i] == Dump::BIGINT && format_bigint_user) {
vformat[i] = new char[strlen(format_bigint_user) + 2];
strcpy(vformat[i],format_bigint_user);
} else {
@ -1085,13 +1084,13 @@ int DumpCustom::convert_string(int n, double *mybuf)
}
for (j = 0; j < size_one; j++) {
if (vtype[j] == INT)
if (vtype[j] == Dump::INT)
offset += sprintf(&sbuf[offset],vformat[j],static_cast<int> (mybuf[m]));
else if (vtype[j] == DOUBLE)
else if (vtype[j] == Dump::DOUBLE)
offset += sprintf(&sbuf[offset],vformat[j],mybuf[m]);
else if (vtype[j] == STRING)
else if (vtype[j] == Dump::STRING)
offset += sprintf(&sbuf[offset],vformat[j],typenames[(int) mybuf[m]]);
else if (vtype[j] == BIGINT)
else if (vtype[j] == Dump::BIGINT)
offset += sprintf(&sbuf[offset],vformat[j],
static_cast<bigint> (mybuf[m]));
m++;
@ -1134,11 +1133,11 @@ void DumpCustom::write_lines(int n, double *mybuf)
int m = 0;
for (i = 0; i < n; i++) {
for (j = 0; j < size_one; j++) {
if (vtype[j] == INT) fprintf(fp,vformat[j],static_cast<int> (mybuf[m]));
else if (vtype[j] == DOUBLE) fprintf(fp,vformat[j],mybuf[m]);
else if (vtype[j] == STRING)
if (vtype[j] == Dump::INT) fprintf(fp,vformat[j],static_cast<int> (mybuf[m]));
else if (vtype[j] == Dump::DOUBLE) fprintf(fp,vformat[j],mybuf[m]);
else if (vtype[j] == Dump::STRING)
fprintf(fp,vformat[j],typenames[(int) mybuf[m]]);
else if (vtype[j] == BIGINT)
else if (vtype[j] == Dump::BIGINT)
fprintf(fp,vformat[j],static_cast<bigint> (mybuf[m]));
m++;
}
@ -1158,191 +1157,192 @@ int DumpCustom::parse_fields(int narg, char **arg)
if (strcmp(arg[iarg],"id") == 0) {
pack_choice[i] = &DumpCustom::pack_id;
if (sizeof(tagint) == sizeof(smallint)) vtype[i] = INT;
else vtype[i] = BIGINT;
if (sizeof(tagint) == sizeof(smallint)) vtype[i] = Dump::INT;
else vtype[i] = Dump::BIGINT;
} else if (strcmp(arg[iarg],"mol") == 0) {
if (!atom->molecule_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_molecule;
if (sizeof(tagint) == sizeof(smallint)) vtype[i] = INT;
else vtype[i] = BIGINT;
if (sizeof(tagint) == sizeof(smallint)) vtype[i] = Dump::INT;
else vtype[i] = Dump::BIGINT;
} else if (strcmp(arg[iarg],"proc") == 0) {
pack_choice[i] = &DumpCustom::pack_proc;
vtype[i] = INT;
vtype[i] = Dump::INT;
} else if (strcmp(arg[iarg],"procp1") == 0) {
pack_choice[i] = &DumpCustom::pack_procp1;
vtype[i] = INT;
vtype[i] = Dump::INT;
} else if (strcmp(arg[iarg],"type") == 0) {
pack_choice[i] = &DumpCustom::pack_type;
vtype[i] = INT;
vtype[i] = Dump::INT;
} else if (strcmp(arg[iarg],"element") == 0) {
pack_choice[i] = &DumpCustom::pack_type;
vtype[i] = STRING;
vtype[i] = Dump::STRING;
} else if (strcmp(arg[iarg],"mass") == 0) {
pack_choice[i] = &DumpCustom::pack_mass;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"x") == 0) {
pack_choice[i] = &DumpCustom::pack_x;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"y") == 0) {
pack_choice[i] = &DumpCustom::pack_y;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"z") == 0) {
pack_choice[i] = &DumpCustom::pack_z;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"xs") == 0) {
if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_xs_triclinic;
else pack_choice[i] = &DumpCustom::pack_xs;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"ys") == 0) {
if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_ys_triclinic;
else pack_choice[i] = &DumpCustom::pack_ys;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"zs") == 0) {
if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_zs_triclinic;
else pack_choice[i] = &DumpCustom::pack_zs;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"xu") == 0) {
if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_xu_triclinic;
else pack_choice[i] = &DumpCustom::pack_xu;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"yu") == 0) {
if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_yu_triclinic;
else pack_choice[i] = &DumpCustom::pack_yu;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"zu") == 0) {
if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_zu_triclinic;
else pack_choice[i] = &DumpCustom::pack_zu;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"xsu") == 0) {
if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_xsu_triclinic;
else pack_choice[i] = &DumpCustom::pack_xsu;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"ysu") == 0) {
if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_ysu_triclinic;
else pack_choice[i] = &DumpCustom::pack_ysu;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"zsu") == 0) {
if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_zsu_triclinic;
else pack_choice[i] = &DumpCustom::pack_zsu;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"ix") == 0) {
pack_choice[i] = &DumpCustom::pack_ix;
vtype[i] = INT;
vtype[i] = Dump::INT;
} else if (strcmp(arg[iarg],"iy") == 0) {
pack_choice[i] = &DumpCustom::pack_iy;
vtype[i] = INT;
vtype[i] = Dump::INT;
} else if (strcmp(arg[iarg],"iz") == 0) {
pack_choice[i] = &DumpCustom::pack_iz;
vtype[i] = INT;
vtype[i] = Dump::INT;
} else if (strcmp(arg[iarg],"vx") == 0) {
pack_choice[i] = &DumpCustom::pack_vx;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"vy") == 0) {
pack_choice[i] = &DumpCustom::pack_vy;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"vz") == 0) {
pack_choice[i] = &DumpCustom::pack_vz;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"fx") == 0) {
pack_choice[i] = &DumpCustom::pack_fx;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"fy") == 0) {
pack_choice[i] = &DumpCustom::pack_fy;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"fz") == 0) {
pack_choice[i] = &DumpCustom::pack_fz;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"q") == 0) {
if (!atom->q_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_q;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"mux") == 0) {
if (!atom->mu_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_mux;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"muy") == 0) {
if (!atom->mu_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_muy;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"muz") == 0) {
if (!atom->mu_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_muz;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"mu") == 0) {
if (!atom->mu_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_mu;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"radius") == 0) {
if (!atom->radius_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_radius;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"diameter") == 0) {
if (!atom->radius_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_diameter;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"omegax") == 0) {
if (!atom->omega_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_omegax;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"omegay") == 0) {
if (!atom->omega_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_omegay;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"omegaz") == 0) {
if (!atom->omega_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_omegaz;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"angmomx") == 0) {
if (!atom->angmom_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_angmomx;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"angmomy") == 0) {
if (!atom->angmom_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_angmomy;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"angmomz") == 0) {
if (!atom->angmom_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_angmomz;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"tqx") == 0) {
if (!atom->torque_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_tqx;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"tqy") == 0) {
if (!atom->torque_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_tqy;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"tqz") == 0) {
if (!atom->torque_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_tqz;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
// compute value = c_ID
// if no trailing [], then arg is set to 0, else arg is int between []
} else if (strncmp(arg[iarg],"c_",2) == 0) {
pack_choice[i] = &DumpCustom::pack_compute;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
@ -1378,7 +1378,7 @@ int DumpCustom::parse_fields(int narg, char **arg)
} else if (strncmp(arg[iarg],"f_",2) == 0) {
pack_choice[i] = &DumpCustom::pack_fix;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
@ -1411,7 +1411,7 @@ int DumpCustom::parse_fields(int narg, char **arg)
} else if (strncmp(arg[iarg],"v_",2) == 0) {
pack_choice[i] = &DumpCustom::pack_variable;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
@ -1431,7 +1431,7 @@ int DumpCustom::parse_fields(int narg, char **arg)
} else if (strncmp(arg[iarg],"d_",2) == 0) {
pack_choice[i] = &DumpCustom::pack_custom;
vtype[i] = DOUBLE;
vtype[i] = Dump::DOUBLE;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
@ -1453,7 +1453,7 @@ int DumpCustom::parse_fields(int narg, char **arg)
} else if (strncmp(arg[iarg],"i_",2) == 0) {
pack_choice[i] = &DumpCustom::pack_custom;
vtype[i] = INT;
vtype[i] = Dump::INT;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
@ -1672,7 +1672,7 @@ int DumpCustom::modify_param(int narg, char **arg)
if (strcmp(arg[0],"refresh") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
if (strncmp(arg[1],"c_",2) != 0)
if (strncmp(arg[1],"c_",2) != 0)
error->all(FLERR,"Illegal dump_modify command");
if (refreshflag) error->all(FLERR,"Dump modify can only have one refresh");