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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8179 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2012-05-24 13:35:09 +00:00
parent b02227547d
commit d1419c4c9c
4 changed files with 96 additions and 14 deletions
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57
src/fix_temp_berendsen.cpp
View File

@ -18,6 +18,8 @@
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "input.h"
#include "variable.h"
#include "group.h"
#include "update.h"
#include "modify.h"
@ -28,6 +30,7 @@ using namespace LAMMPS_NS;
using namespace FixConst;
enum{NOBIAS,BIAS};
enum{CONSTANT,EQUAL};
/* ---------------------------------------------------------------------- */
@ -43,14 +46,25 @@ FixTempBerendsen::FixTempBerendsen(LAMMPS *lmp, int narg, char **arg) :
global_freq = nevery;
extscalar = 1;
t_start = atof(arg[3]);
t_target = t_start;
tstr = NULL;
if (strstr(arg[3],"v_") == arg[3]) {
int n = strlen(&arg[3][2]) + 1;
tstr = new char[n];
strcpy(tstr,&arg[3][2]);
tstyle = EQUAL;
} else {
t_start = atof(arg[3]);
t_target = t_start;
tstyle = CONSTANT;
}
t_stop = atof(arg[4]);
t_period = atof(arg[5]);
// error checks
if (t_period <= 0.0) error->all(FLERR,"Fix temp/berendsen period must be > 0.0");
if (t_period <= 0.0)
error->all(FLERR,"Fix temp/berendsen period must be > 0.0");
// create a new compute temp style
// id = fix-ID + temp, compute group = fix group
@ -75,6 +89,8 @@ FixTempBerendsen::FixTempBerendsen(LAMMPS *lmp, int narg, char **arg) :
FixTempBerendsen::~FixTempBerendsen()
{
delete [] tstr;
// delete temperature if fix created it
if (tflag) modify->delete_compute(id_temp);
@ -95,6 +111,16 @@ int FixTempBerendsen::setmask()
void FixTempBerendsen::init()
{
// check variable
if (tstr) {
tvar = input->variable->find(tstr);
if (tvar < 0)
error->all(FLERR,"Variable name for fix temp/berendsen does not exist");
if (input->variable->equalstyle(tvar)) tstyle = EQUAL;
else error->all(FLERR,"Variable for fix temp/berendsen is invalid style");
}
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
error->all(FLERR,"Temperature ID for fix temp/berendsen does not exist");
@ -110,11 +136,25 @@ void FixTempBerendsen::end_of_step()
{
double t_current = temperature->compute_scalar();
if (t_current == 0.0)
error->all(FLERR,"Computed temperature for fix temp/berendsen cannot be 0.0");
error->all(FLERR,
"Computed temperature for fix temp/berendsen cannot be 0.0");
double delta = update->ntimestep - update->beginstep;
delta /= update->endstep - update->beginstep;
t_target = t_start + delta * (t_stop-t_start);
// set current t_target
// if variable temp, evaluate variable, wrap with clear/add
if (tstyle == CONSTANT)
t_target = t_start + delta * (t_stop-t_start);
else {
modify->clearstep_compute();
t_target = input->variable->compute_equal(tvar);
if (t_target < 0.0)
error->one(FLERR,
"Fix temp/berendsen variable returned negative temperature");
modify->addstep_compute(update->ntimestep + nevery);
}
// rescale velocities by lamda
// for BIAS:
@ -166,11 +206,13 @@ int FixTempBerendsen::modify_param(int narg, char **arg)
strcpy(id_temp,arg[1]);
int icompute = modify->find_compute(id_temp);
if (icompute < 0) error->all(FLERR,"Could not find fix_modify temperature ID");
if (icompute < 0)
error->all(FLERR,"Could not find fix_modify temperature ID");
temperature = modify->compute[icompute];
if (temperature->tempflag == 0)
error->all(FLERR,"Fix_modify temperature ID does not compute temperature");
error->all(FLERR,
"Fix_modify temperature ID does not compute temperature");
if (temperature->igroup != igroup && comm->me == 0)
error->warning(FLERR,"Group for fix_modify temp != fix group");
return 2;
@ -204,4 +246,3 @@ void *FixTempBerendsen::extract(const char *str, int &dim)
}
return NULL;
}

2
src/fix_temp_berendsen.h
View File

@ -40,6 +40,8 @@ class FixTempBerendsen : public Fix {
int which;
double t_start,t_stop,t_period,t_target;
double energy;
int tstyle,tvar;
char *tstr;
char *id_temp;
class Compute *temperature;

49
src/fix_temp_rescale.cpp
View File

@ -22,6 +22,8 @@
#include "domain.h"
#include "region.h"
#include "comm.h"
#include "input.h"
#include "variable.h"
#include "modify.h"
#include "compute.h"
#include "error.h"
@ -30,6 +32,7 @@ using namespace LAMMPS_NS;
using namespace FixConst;
enum{NOBIAS,BIAS};
enum{CONSTANT,EQUAL};
/* ---------------------------------------------------------------------- */
@ -45,8 +48,18 @@ FixTempRescale::FixTempRescale(LAMMPS *lmp, int narg, char **arg) :
global_freq = nevery;
extscalar = 1;
t_start = atof(arg[4]);
t_target = t_start;
tstr = NULL;
if (strstr(arg[4],"v_") == arg[4]) {
int n = strlen(&arg[4][2]) + 1;
tstr = new char[n];
strcpy(tstr,&arg[4][2]);
tstyle = EQUAL;
} else {
t_start = atof(arg[4]);
t_target = t_start;
tstyle = CONSTANT;
}
t_stop = atof(arg[5]);
t_window = atof(arg[6]);
fraction = atof(arg[7]);
@ -74,6 +87,8 @@ FixTempRescale::FixTempRescale(LAMMPS *lmp, int narg, char **arg) :
FixTempRescale::~FixTempRescale()
{
delete [] tstr;
// delete temperature if fix created it
if (tflag) modify->delete_compute(id_temp);
@ -94,6 +109,16 @@ int FixTempRescale::setmask()
void FixTempRescale::init()
{
// check variable
if (tstr) {
tvar = input->variable->find(tstr);
if (tvar < 0)
error->all(FLERR,"Variable name for fix temp/rescale does not exist");
if (input->variable->equalstyle(tvar)) tstyle = EQUAL;
else error->all(FLERR,"Variable for fix temp/rescale is invalid style");
}
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
error->all(FLERR,"Temperature ID for fix temp/rescale does not exist");
@ -113,7 +138,20 @@ void FixTempRescale::end_of_step()
double delta = update->ntimestep - update->beginstep;
delta /= update->endstep - update->beginstep;
t_target = t_start + delta * (t_stop-t_start);
// set current t_target and t_sqrt
// if variable temp, evaluate variable, wrap with clear/add
if (tstyle == CONSTANT)
t_target = t_start + delta * (t_stop-t_start);
else {
modify->clearstep_compute();
t_target = input->variable->compute_equal(tvar);
if (t_target < 0.0)
error->one(FLERR,
"Fix temp/rescale variable returned negative temperature");
modify->addstep_compute(update->ntimestep + nevery);
}
// rescale velocity of appropriate atoms if outside window
// for BIAS:
@ -150,7 +188,6 @@ void FixTempRescale::end_of_step()
}
}
}
}
}
@ -175,7 +212,8 @@ int FixTempRescale::modify_param(int narg, char **arg)
temperature = modify->compute[icompute];
if (temperature->tempflag == 0)
error->all(FLERR,"Fix_modify temperature ID does not compute temperature");
error->all(FLERR,
"Fix_modify temperature ID does not compute temperature");
if (temperature->igroup != igroup && comm->me == 0)
error->warning(FLERR,"Group for fix_modify temp != fix group");
return 2;
@ -209,4 +247,3 @@ void *FixTempRescale::extract(const char *str, int &dim)
}
return NULL;
}

2
src/fix_temp_rescale.h
View File

@ -40,6 +40,8 @@ class FixTempRescale : public Fix {
int which;
double t_start,t_stop,t_window,t_target;
double fraction,energy,efactor;
int tstyle,tvar;
char *tstr;
char *id_temp;
class Compute *temperature;