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Merge branch 'master' into thermo-energy

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# Conflicts:
#	doc/src/fix_ti_spring.rst
#	src/RIGID/fix_rigid_small.cpp
#	src/fix_langevin.cpp
#	src/fix_temp_berendsen.cpp
#	src/fix_temp_csld.cpp
#	src/fix_temp_csvr.cpp
#	src/fix_temp_rescale.cpp
#	src/thermo.cpp
This commit is contained in:
Axel Kohlmeyer
2021-02-08 15:18:04 -05:00
parent bca3164fc4 a3a84c4493
commit 33939a0e26
1318 changed files with 36902 additions and 51251 deletions
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26
src/RIGID/fix_rigid.cpp
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@ -127,7 +127,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
// determine whether atom-style variable or atom property is used
if (strstr(arg[4],"i_") == arg[4]) {
if (utils::strmatch(arg[4],"^i_")) {
int is_double=0;
int custom_index = atom->find_custom(arg[4]+2,is_double);
if (custom_index == -1)
@ -149,7 +149,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
else
molecule[i] = 0;
} else if (strstr(arg[4],"v_") == arg[4]) {
} else if (utils::strmatch(arg[4],"^v_")) {
int ivariable = input->variable->find(arg[4]+2);
if (ivariable < 0)
error->all(FLERR,"Variable name for fix rigid custom does not exist");
@ -500,9 +500,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
else {
allremap = 0;
delete [] id_dilate;
int n = strlen(arg[iarg+1]) + 1;
id_dilate = new char[n];
strcpy(id_dilate,arg[iarg+1]);
id_dilate = utils::strdup(arg[iarg+1]);
int idilate = group->find(id_dilate);
if (idilate == -1)
error->all(FLERR,
@ -529,9 +527,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"infile") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid command");
delete [] inpfile;
int n = strlen(arg[iarg+1]) + 1;
inpfile = new char[n];
strcpy(inpfile,arg[iarg+1]);
inpfile = utils::strdup(arg[iarg+1]);
restart_file = 1;
reinitflag = 0;
iarg += 2;
@ -546,9 +542,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"gravity") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid command");
delete [] id_gravity;
int n = strlen(arg[iarg+1]) + 1;
id_gravity = new char[n];
strcpy(id_gravity,arg[iarg+1]);
id_gravity = utils::strdup(arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal fix rigid command");
@ -2448,12 +2442,12 @@ void FixRigid::write_restart_file(const char *file)
double FixRigid::memory_usage()
{
int nmax = atom->nmax;
double bytes = nmax * sizeof(int);
bytes += nmax * sizeof(imageint);
bytes += nmax*3 * sizeof(double);
bytes += maxvatom*6 * sizeof(double); // vatom
double bytes = (double)nmax * sizeof(int);
bytes += (double)nmax * sizeof(imageint);
bytes += (double)nmax*3 * sizeof(double);
bytes += (double)maxvatom*6 * sizeof(double); // vatom
if (extended) {
bytes += nmax * sizeof(int);
bytes += (double)nmax * sizeof(int);
if (orientflag) bytes = nmax*orientflag * sizeof(double);
if (dorientflag) bytes = nmax*3 * sizeof(double);
}