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retrieve target temperature and pressure from fix npt. add sanity checks.

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This commit is contained in:
Axel Kohlmeyer
2016-11-13 23:18:59 -05:00
parent 26870f223d
commit 14c7cf4197
4 changed files with 66 additions and 13 deletions
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2
examples/USER/misc/grem/lj-single/in.gREM
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@ -14,7 +14,7 @@ thermo_style custom step temp pe etotal press vol
timestep 1.0
fix fxnvt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0
fix fxgREM all grem 400 -.01 -30000 ${T0} ${press}
fix fxgREM all grem 400 -.01 -30000 fxnvt
thermo_modify press fxgREM_press
fix_modify fxnvt press fxgREM_press
run 1000

60
src/USER-MISC/fix_grem.cpp
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@ -47,7 +47,7 @@ enum{NONE,CONSTANT,EQUAL,ATOM};
FixGrem::FixGrem(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 8) error->all(FLERR,"Illegal fix grem command");
if (narg < 7) error->all(FLERR,"Illegal fix grem command");
scalar_flag = 1;
vector_flag = 1;
@ -61,15 +61,17 @@ FixGrem::FixGrem(LAMMPS *lmp, int narg, char **arg) :
lambda = force->numeric(FLERR,arg[3]);
eta = force->numeric(FLERR,arg[4]);
h0 = force->numeric(FLERR,arg[5]);
tbath = force->numeric(FLERR,arg[6]);
pressref = force->numeric(FLERR,arg[7]);
int n = strlen(arg[6])+1;
id_npt = new char[n];
strcpy(id_npt,arg[6]);
// create a new compute temp style
// id = fix-ID + temp
// compute group = all since pressure is always global (group all)
// and thus its KE/temperature contribution should use group all
int n = strlen(id) + 6;
n = strlen(id) + 6;
id_temp = new char[n];
strcpy(id_temp,id);
strcat(id_temp,"_temp");
@ -148,7 +150,7 @@ FixGrem::~FixGrem()
delete [] id_press;
delete [] id_ke;
delete [] id_pe;
delete [] id_npt;
}
/* ---------------------------------------------------------------------- */
@ -165,24 +167,61 @@ int FixGrem::setmask()
void FixGrem::init()
{
// add check of sign of eta
if (domain->triclinic)
error->all(FLERR,"Triclinic cells are not supported");
// set temperature and pressure ptrs
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
error->all(FLERR,"Temperature ID for fix scaledforce does not exist");
error->all(FLERR,"Temperature compute ID for fix grem does not exist");
temperature = modify->compute[icompute];
icompute = modify->find_compute(id_ke);
if (icompute < 0)
error->all(FLERR,"Ke ID for fix scaledforce does not exist");
error->all(FLERR,"KE compute ID for fix grem does not exist");
ke = modify->compute[icompute];
icompute = modify->find_compute(id_pe);
if (icompute < 0)
error->all(FLERR,"Pe ID for fix scaledforce does not exist");
error->all(FLERR,"PE compute ID for fix grem does not exist");
pe = modify->compute[icompute];
int ifix = modify->find_fix(id_npt);
if (ifix < 0)
error->all(FLERR,"Fix id for npt fix does not exist");
Fix *npt = modify->fix[ifix];
double *t_start = (double *)npt->extract("t_start",ifix);
double *t_stop = (double *)npt->extract("t_stop",ifix);
if ((t_start != NULL) && (t_stop != NULL) && (ifix == 0)) {
tbath = *t_start;
if (*t_start != *t_stop)
error->all(FLERR,"Thermostat temperature ramp not allowed");
} else
error->all(FLERR,"Problem extracting target temperature from fix npt");
int *p_flag = (int *)npt->extract("p_flag",ifix);
double *p_start = (double *) npt->extract("p_start",ifix);
double *p_stop = (double *) npt->extract("p_stop",ifix);
if ((p_flag != NULL) && (p_start != NULL) && (p_stop != NULL)
&& (ifix == 1)) {
ifix = 0;
pressref = p_start[0];
if ((p_start[0] != p_stop[0]) || (p_flag[0] != 1)) ++ ifix;
if ((p_start[1] != p_stop[1]) || (p_flag[0] != 1)) ++ ifix;
if ((p_start[2] != p_stop[2]) || (p_flag[0] != 1)) ++ ifix;
if ((p_start[0] != p_start[1]) || (p_start[1] != p_start[2])) ++ifix;
if ((p_flag[3] != 0) || (p_flag[4] != 0) || (p_flag[5] != 0)) ++ifix;
if (ifix > 0)
error->all(FLERR,"Unsupported pressure settings in fix npt");
} else
error->all(FLERR,"Problem extracting target pressure from fix npt");
char *modargs[2];
modargs[0] = (char *) "press";
modargs[1] = id_press;
npt->modify_param(2,modargs);
}
/* ---------------------------------------------------------------------- */
@ -191,6 +230,9 @@ void FixGrem::setup(int vflag)
{
if (strstr(update->integrate_style,"verlet"))
post_force(vflag);
if (strstr(update->integrate_style,"respa"))
error->all(FLERR,"Run style 'respa' is not supported");
}
/* ---------------------------------------------------------------------- */

3
src/USER-MISC/fix_grem.h
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@ -40,10 +40,9 @@ class FixGrem : public Fix {
double lambda,eta,h0,tbath,pressref;
protected:
char *id_temp,*id_press,*id_ke,*id_pe;
char *id_temp,*id_press,*id_ke,*id_pe,*id_npt;
class Compute *temperature,*pressure,*ke,*pe;
int pflag,tflag,keflag,peflag;
};
}

12
src/fix_nh.cpp
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@ -1700,12 +1700,24 @@ void *FixNH::extract(const char *str, int &dim)
dim=0;
if (strcmp(str,"t_target") == 0) {
return &t_target;
} else if (strcmp(str,"t_start") == 0) {
return &t_start;
} else if (strcmp(str,"t_stop") == 0) {
return &t_stop;
} else if (strcmp(str,"mtchain") == 0) {
return &mtchain;
}
dim=1;
if (strcmp(str,"eta") == 0) {
return &eta;
} else if (strcmp(str,"p_flag") == 0) {
return &p_flag;
} else if (strcmp(str,"p_start") == 0) {
return &p_start;
} else if (strcmp(str,"p_stop") == 0) {
return &p_stop;
} else if (strcmp(str,"p_target") == 0) {
return &p_target;
}
return NULL;
}