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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10985 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2013-11-06 19:00:54 +00:00
parent aa9502ec5a
commit faff0eb70b
4 changed files with 722 additions and 704 deletions
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4
src/USER-MISC/fix_ti_rs.cpp
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@ -45,8 +45,8 @@ FixTIRS::FixTIRS(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
extvector = 1;
// Time variables.
t_switch = atof(arg[5]);
t_equil = atof(arg[6]);
t_switch = atoi(arg[5]);
t_equil = atoi(arg[6]);
t0 = update->ntimestep;
if (t_switch < 0.0) error->all(FLERR,"Illegal fix ti/rs command");
if (t_equil < 0.0) error->all(FLERR,"Illegal fix ti/rs command");

6
src/USER-MISC/fix_ti_rs.h
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@ -11,6 +11,12 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors:
Rodrigo Freitas (Unicamp/Brazil) - rodrigohb@gmail.com
Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(ti/rs,FixTIRS)

32
src/USER-MISC/fix_ti_spring.cpp
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@ -26,20 +26,23 @@
#include "respa.h"
#include "memory.h"
#include "error.h"
#include "force.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixTISpring::FixTISpring(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) {
FixTISpring::FixTISpring(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 6 || narg > 8)
error->all(FLERR,"Illegal fix ti/spring command");
// Flags.
restart_peratom = 1;
scalar_flag = 1;
global_freq = 1;
vector_flag = 1;
size_vector = 2;
global_freq = 1;
@ -47,29 +50,31 @@ FixTISpring::FixTISpring(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg
extvector = 1;
// Spring constant.
k = atof(arg[3]);
espring = 0.0;
k = force->numeric(FLERR,arg[3]);
if (k <= 0.0) error->all(FLERR,"Illegal fix ti/spring command");
// Initial position.
// Perform initial allocation of atom-based array.
// Registar with Atom class.
xoriginal = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
atom->add_callback(1);
// xoriginal = initial unwrapped positions of atom.
double **x = atom->x;
int *mask = atom->mask;
tagint *image = atom->image;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) domain->unmap(x[i], image[i], xoriginal[i]);
if (mask[i] & groupbit) domain->unmap(x[i],image[i],xoriginal[i]);
else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
}
// Time variables.
t_switch = atof(arg[4]); // Switching time.
t_equil = atof(arg[5]); // Equilibration time.
t_switch = atoi(arg[4]); // Switching time.
t_equil = atoi(arg[5]); // Equilibration time.
t0 = update->ntimestep; // Initial time.
if (t_switch < 0.0) error->all(FLERR,"Illegal fix ti/spring command");
if (t_equil < 0.0) error->all(FLERR,"Illegal fix ti/spring command");
@ -84,6 +89,8 @@ FixTISpring::FixTISpring(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg
}
lambda = switch_func(0);
dlambda = dswitch_func(0);
espring = 0.0;
}
/* ---------------------------------------------------------------------- */
@ -143,10 +150,8 @@ void FixTISpring::min_setup(int vflag)
void FixTISpring::post_force(int vflag)
{
// If on the first equilibration do not calculate forces.
int t = update->ntimestep - t0;
espring = 0.0;
if(t < t_equil) return;
double **x = atom->x;
@ -158,9 +163,11 @@ void FixTISpring::post_force(int vflag)
double dx, dy, dz;
double unwrap[3];
espring = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
domain->unmap(x[i], image[i], unwrap);
domain->unmap(x[i],image[i],unwrap);
dx = unwrap[0] - xoriginal[i][0];
dy = unwrap[1] - xoriginal[i][1];
dz = unwrap[2] - xoriginal[i][2];
@ -250,7 +257,7 @@ void FixTISpring::grow_arrays(int nmax)
copy values within local atom-based array
------------------------------------------------------------------------- */
void FixTISpring::copy_arrays(int i, int j)
void FixTISpring::copy_arrays(int i, int j, int delflag)
{
xoriginal[j][0] = xoriginal[i][0];
xoriginal[j][1] = xoriginal[i][1];
@ -294,7 +301,6 @@ int FixTISpring::pack_restart(int i, double *buf)
return 4;
}
/* ----------------------------------------------------------------------
unpack values from atom->extra array to restart the fix
------------------------------------------------------------------------- */

8
src/USER-MISC/fix_ti_spring.h
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@ -11,6 +11,12 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors:
Rodrigo Freitas (Unicamp/Brazil) - rodrigohb@gmail.com
Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(ti/spring,FixTISpring)
@ -41,7 +47,7 @@ class FixTISpring : public Fix {
double memory_usage();
void grow_arrays(int);
void copy_arrays(int, int);
void copy_arrays(int, int, int);
int pack_exchange(int, double *);
int unpack_exchange(int, double *);
int pack_restart(int, double *);