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some applications of the new function

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This commit is contained in:
Axel Kohlmeyer
2021-09-19 19:05:40 -04:00
parent 860a93aa8b
commit f80259dfae
7 changed files with 30 additions and 66 deletions
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24
src/read_dump.cpp
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@ -1217,27 +1217,19 @@ int ReadDump::fields_and_keywords(int narg, char **arg)
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"box") == 0) { } else if (strcmp(arg[iarg],"box") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command"); if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command");
if (strcmp(arg[iarg+1],"yes") == 0) boxflag = 1; boxflag = utils::logical(FLERR,arg[iarg+1],false,lmp);
else if (strcmp(arg[iarg+1],"no") == 0) boxflag = 0;
else error->all(FLERR,"Illegal read_dump command");
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"replace") == 0) { } else if (strcmp(arg[iarg],"replace") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command"); if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command");
if (strcmp(arg[iarg+1],"yes") == 0) replaceflag = 1; replaceflag = utils::logical(FLERR,arg[iarg+1],false,lmp);
else if (strcmp(arg[iarg+1],"no") == 0) replaceflag = 0;
else error->all(FLERR,"Illegal read_dump command");
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"purge") == 0) { } else if (strcmp(arg[iarg],"purge") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command"); if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command");
if (strcmp(arg[iarg+1],"yes") == 0) purgeflag = 1; purgeflag = utils::logical(FLERR,arg[iarg+1],false,lmp);
else if (strcmp(arg[iarg+1],"no") == 0) purgeflag = 0;
else error->all(FLERR,"Illegal read_dump command");
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"trim") == 0) { } else if (strcmp(arg[iarg],"trim") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command"); if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command");
if (strcmp(arg[iarg+1],"yes") == 0) trimflag = 1; trimflag = utils::logical(FLERR,arg[iarg+1],false,lmp);
else if (strcmp(arg[iarg+1],"no") == 0) trimflag = 0;
else error->all(FLERR,"Illegal read_dump command");
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"add") == 0) { } else if (strcmp(arg[iarg],"add") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command"); if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command");
@ -1257,15 +1249,11 @@ int ReadDump::fields_and_keywords(int narg, char **arg)
iarg += 3; iarg += 3;
} else if (strcmp(arg[iarg],"scaled") == 0) { } else if (strcmp(arg[iarg],"scaled") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command"); if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command");
if (strcmp(arg[iarg+1],"yes") == 0) scaleflag = 1; scaleflag = utils::logical(FLERR,arg[iarg+1],false,lmp);
else if (strcmp(arg[iarg+1],"no") == 0) scaleflag = 0;
else error->all(FLERR,"Illegal read_dump command");
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"wrapped") == 0) { } else if (strcmp(arg[iarg],"wrapped") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command"); if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command");
if (strcmp(arg[iarg+1],"yes") == 0) wrapflag = 1; wrapflag = utils::logical(FLERR,arg[iarg+1],false,lmp);
else if (strcmp(arg[iarg+1],"no") == 0) wrapflag = 0;
else error->all(FLERR,"Illegal read_dump command");
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"format") == 0) { } else if (strcmp(arg[iarg],"format") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command"); if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command");

6
src/rerun.cpp
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@ -106,11 +106,7 @@ void Rerun::command(int narg, char **arg)
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"post") == 0) { } else if (strcmp(arg[iarg],"post") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal rerun command"); if (iarg+2 > narg) error->all(FLERR,"Illegal rerun command");
if (strcmp(arg[iarg+1],"yes") == 0) { postflag = utils::logical(FLERR,arg[iarg+1],false,lmp);
postflag = 1;
} else if (strcmp(arg[iarg+1],"no") == 0) {
postflag = 0;
} else error->all(FLERR,"Illegal rerun command");
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"dump") == 0) { } else if (strcmp(arg[iarg],"dump") == 0) {
break; break;

4
src/reset_atom_ids.cpp
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@ -69,9 +69,7 @@ void ResetIDs::command(int narg, char **arg)
while (iarg < narg) { while (iarg < narg) {
if (strcmp(arg[iarg],"sort") == 0) { if (strcmp(arg[iarg],"sort") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal reset_atom_ids command"); if (iarg+2 > narg) error->all(FLERR,"Illegal reset_atom_ids command");
if (strcmp(arg[iarg+1],"yes") == 0) sortflag = 1; sortflag = utils::logical(FLERR,arg[iarg+1],false,lmp);
else if (strcmp(arg[iarg+1],"no") == 0) sortflag = 0;
else error->all(FLERR,"Illegal reset_atom_ids command");
iarg += 2; iarg += 2;
} else error->all(FLERR,"Illegal reset_atom_ids command"); } else error->all(FLERR,"Illegal reset_atom_ids command");
} }

8
src/reset_mol_ids.cpp
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@ -77,15 +77,11 @@ void ResetMolIDs::command(int narg, char **arg)
while (iarg < narg) { while (iarg < narg) {
if (strcmp(arg[iarg],"compress") == 0) { if (strcmp(arg[iarg],"compress") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal reset_mol_ids command"); if (iarg+2 > narg) error->all(FLERR,"Illegal reset_mol_ids command");
if (strcmp(arg[iarg+1],"yes") == 0) compressflag = 1; compressflag = utils::logical(FLERR,arg[iarg+1],false,lmp);
else if (strcmp(arg[iarg+1],"no") == 0) compressflag = 0;
else error->all(FLERR,"Illegal reset_mol_ids command");
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"single") == 0) { } else if (strcmp(arg[iarg],"single") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal reset_mol_ids command"); if (iarg+2 > narg) error->all(FLERR,"Illegal reset_mol_ids command");
if (strcmp(arg[iarg+1],"yes") == 0) singleflag = 1; singleflag = utils::logical(FLERR,arg[iarg+1],false,lmp);
else if (strcmp(arg[iarg+1],"no") == 0) singleflag = 0;
else error->all(FLERR,"Illegal reset_mol_ids command");
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"offset") == 0) { } else if (strcmp(arg[iarg],"offset") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal reset_mol_ids command"); if (iarg+2 > narg) error->all(FLERR,"Illegal reset_mol_ids command");

8
src/run.cpp
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@ -77,15 +77,11 @@ void Run::command(int narg, char **arg)
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"pre") == 0) { } else if (strcmp(arg[iarg],"pre") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal run command"); if (iarg+2 > narg) error->all(FLERR,"Illegal run command");
if (strcmp(arg[iarg+1],"no") == 0) preflag = 0; preflag = utils::logical(FLERR,arg[iarg+1],false,lmp);
else if (strcmp(arg[iarg+1],"yes") == 0) preflag = 1;
else error->all(FLERR,"Illegal run command");
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"post") == 0) { } else if (strcmp(arg[iarg],"post") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal run command"); if (iarg+2 > narg) error->all(FLERR,"Illegal run command");
if (strcmp(arg[iarg+1],"no") == 0) postflag = 0; postflag = utils::logical(FLERR,arg[iarg+1],false,lmp);
else if (strcmp(arg[iarg+1],"yes") == 0) postflag = 1;
else error->all(FLERR,"Illegal run command");
iarg += 2; iarg += 2;
// all remaining args are commands // all remaining args are commands

8
src/thermo.cpp
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@ -556,16 +556,12 @@ void Thermo::modify_params(int narg, char **arg)
} else if (strcmp(arg[iarg],"norm") == 0) { } else if (strcmp(arg[iarg],"norm") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal thermo_modify command"); if (iarg+2 > narg) error->all(FLERR,"Illegal thermo_modify command");
normuserflag = 1; normuserflag = 1;
if (strcmp(arg[iarg+1],"no") == 0) normuser = 0; normuser = utils::logical(FLERR,arg[iarg+1],false,lmp);
else if (strcmp(arg[iarg+1],"yes") == 0) normuser = 1;
else error->all(FLERR,"Illegal thermo_modify command");
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"flush") == 0) { } else if (strcmp(arg[iarg],"flush") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal thermo_modify command"); if (iarg+2 > narg) error->all(FLERR,"Illegal thermo_modify command");
if (strcmp(arg[iarg+1],"no") == 0) flushflag = 0; flushflag = utils::logical(FLERR,arg[iarg+1],false,lmp);
else if (strcmp(arg[iarg+1],"yes") == 0) flushflag = 1;
else error->all(FLERR,"Illegal thermo_modify command");
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"line") == 0) { } else if (strcmp(arg[iarg],"line") == 0) {

38
src/velocity.cpp
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@ -36,6 +36,7 @@ using namespace LAMMPS_NS;
enum{CREATE,SET,SCALE,RAMP,ZERO}; enum{CREATE,SET,SCALE,RAMP,ZERO};
enum{ALL,LOCAL,GEOM}; enum{ALL,LOCAL,GEOM};
enum{UNIFORM,GAUSSIAN};
enum{NONE,CONSTANT,EQUAL,ATOM}; enum{NONE,CONSTANT,EQUAL,ATOM};
#define WARMUP 100 #define WARMUP 100
@ -84,7 +85,7 @@ void Velocity::command(int narg, char **arg)
// set defaults // set defaults
temperature = nullptr; temperature = nullptr;
dist_flag = 0; dist_flag = UNIFORM;
sum_flag = 0; sum_flag = 0;
momentum_flag = 1; momentum_flag = 1;
rotation_flag = 0; rotation_flag = 0;
@ -149,11 +150,12 @@ void Velocity::init_external(const char *extgroup)
groupbit = group->bitmask[igroup]; groupbit = group->bitmask[igroup];
temperature = nullptr; temperature = nullptr;
dist_flag = 0; dist_flag = UNIFORM;
sum_flag = 0; sum_flag = 0;
momentum_flag = 1; momentum_flag = 1;
rotation_flag = 0; rotation_flag = 0;
loop_flag = ALL; loop_flag = ALL;
rfix = -1;
scale_flag = 1; scale_flag = 1;
bias_flag = 0; bias_flag = 0;
} }
@ -275,11 +277,11 @@ void Velocity::create(double t_desired, int seed)
int natoms = static_cast<int> (atom->natoms); int natoms = static_cast<int> (atom->natoms);
for (i = 1; i <= natoms; i++) { for (i = 1; i <= natoms; i++) {
if (dist_flag == 0) { if (dist_flag == UNIFORM) {
vx = random->uniform() - 0.5; vx = random->uniform() - 0.5;
vy = random->uniform() - 0.5; vy = random->uniform() - 0.5;
vz = random->uniform() - 0.5; vz = random->uniform() - 0.5;
} else { } else { // GAUSSIAN
vx = random->gaussian(); vx = random->gaussian();
vy = random->gaussian(); vy = random->gaussian();
vz = random->gaussian(); vz = random->gaussian();
@ -310,11 +312,11 @@ void Velocity::create(double t_desired, int seed)
for (i = 0; i < nlocal; i++) { for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) { if (mask[i] & groupbit) {
if (dist_flag == 0) { if (dist_flag == UNIFORM) {
vx = random->uniform() - 0.5; vx = random->uniform() - 0.5;
vy = random->uniform() - 0.5; vy = random->uniform() - 0.5;
vz = random->uniform() - 0.5; vz = random->uniform() - 0.5;
} else { } else { // GAUSSIAN
vx = random->gaussian(); vx = random->gaussian();
vy = random->gaussian(); vy = random->gaussian();
vz = random->gaussian(); vz = random->gaussian();
@ -335,11 +337,11 @@ void Velocity::create(double t_desired, int seed)
for (i = 0; i < nlocal; i++) { for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) { if (mask[i] & groupbit) {
random->reset(seed,x[i]); random->reset(seed,x[i]);
if (dist_flag == 0) { if (dist_flag == UNIFORM) {
vx = random->uniform() - 0.5; vx = random->uniform() - 0.5;
vy = random->uniform() - 0.5; vy = random->uniform() - 0.5;
vz = random->uniform() - 0.5; vz = random->uniform() - 0.5;
} else { } else { // GAUSSIAN
vx = random->gaussian(); vx = random->gaussian();
vy = random->gaussian(); vy = random->gaussian();
vz = random->gaussian(); vz = random->gaussian();
@ -824,27 +826,21 @@ void Velocity::options(int narg, char **arg)
while (iarg < narg) { while (iarg < narg) {
if (strcmp(arg[iarg],"dist") == 0) { if (strcmp(arg[iarg],"dist") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal velocity command"); if (iarg+2 > narg) error->all(FLERR,"Illegal velocity command");
if (strcmp(arg[iarg+1],"uniform") == 0) dist_flag = 0; if (strcmp(arg[iarg+1],"uniform") == 0) dist_flag = UNIFORM;
else if (strcmp(arg[iarg+1],"gaussian") == 0) dist_flag = 1; else if (strcmp(arg[iarg+1],"gaussian") == 0) dist_flag = GAUSSIAN;
else error->all(FLERR,"Illegal velocity command"); else error->all(FLERR,"Illegal velocity command");
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"sum") == 0) { } else if (strcmp(arg[iarg],"sum") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal velocity command"); if (iarg+2 > narg) error->all(FLERR,"Illegal velocity command");
if (strcmp(arg[iarg+1],"no") == 0) sum_flag = 0; sum_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
else if (strcmp(arg[iarg+1],"yes") == 0) sum_flag = 1;
else error->all(FLERR,"Illegal velocity command");
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"mom") == 0) { } else if (strcmp(arg[iarg],"mom") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal velocity command"); if (iarg+2 > narg) error->all(FLERR,"Illegal velocity command");
if (strcmp(arg[iarg+1],"no") == 0) momentum_flag = 0; momentum_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
else if (strcmp(arg[iarg+1],"yes") == 0) momentum_flag = 1;
else error->all(FLERR,"Illegal velocity command");
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"rot") == 0) { } else if (strcmp(arg[iarg],"rot") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal velocity command"); if (iarg+2 > narg) error->all(FLERR,"Illegal velocity command");
if (strcmp(arg[iarg+1],"no") == 0) rotation_flag = 0; rotation_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
else if (strcmp(arg[iarg+1],"yes") == 0) rotation_flag = 1;
else error->all(FLERR,"Illegal velocity command");
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"temp") == 0) { } else if (strcmp(arg[iarg],"temp") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal velocity command"); if (iarg+2 > narg) error->all(FLERR,"Illegal velocity command");
@ -856,9 +852,7 @@ void Velocity::options(int narg, char **arg)
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"bias") == 0) { } else if (strcmp(arg[iarg],"bias") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal velocity command"); if (iarg+2 > narg) error->all(FLERR,"Illegal velocity command");
if (strcmp(arg[iarg+1],"no") == 0) bias_flag = 0; bias_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
else if (strcmp(arg[iarg+1],"yes") == 0) bias_flag = 1;
else error->all(FLERR,"Illegal velocity command");
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"loop") == 0) { } else if (strcmp(arg[iarg],"loop") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal velocity command"); if (iarg+2 > narg) error->all(FLERR,"Illegal velocity command");