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add support for fix_modify virial yes to fix smd

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This commit is contained in:
Axel Kohlmeyer
2017-09-15 01:21:16 -04:00
parent ccb67d8dc5
commit 99e5dc7104
2 changed files with 34 additions and 0 deletions
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5
doc/src/fix_smd.txt
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@ -101,6 +101,11 @@ See the "read_restart"_read_restart.html command for info on how to
re-specify a fix in an input script that reads a restart file, so that
the operation of the fix continues in an uninterrupted fashion.
The "fix_modify"_fix_modify.html {virial} option is supported by this
fix to add the contribution due to the added forces on atoms to the
system's virial as part of "thermodynamic output"_thermo_style.html.
The default is {virial no}
The "fix_modify"_fix_modify.html {respa} option is supported by
this fix. This allows to set at which level of the "r-RESPA"_run_style.html
integrator the fix is adding its forces. Default is the outermost level.

29
src/USER-MISC/fix_smd.cpp
View File

@ -58,6 +58,7 @@ FixSMD::FixSMD(LAMMPS *lmp, int narg, char **arg) :
extvector = 1;
respa_level_support = 1;
ilevel_respa = 0;
virial_flag = 1;
int argoffs=3;
if (strcmp(arg[argoffs],"cvel") == 0) {
@ -181,6 +182,11 @@ void FixSMD::setup(int vflag)
void FixSMD::post_force(int vflag)
{
// energy and virial setup
if (vflag) v_setup(vflag);
else evflag = 0;
if (styleflag & SMD_TETHER) smd_tether();
else smd_couple();
@ -238,12 +244,15 @@ void FixSMD::smd_tether()
// apply restoring force to atoms in group
// f = -k*(r-r0)*mass/masstotal
double **x = atom->x;
double **f = atom->f;
imageint *image = atom->image;
int *mask = atom->mask;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
double massfrac;
double unwrap[3],v[6];
int nlocal = atom->nlocal;
ftotal[0] = ftotal[1] = ftotal[2] = 0.0;
@ -259,6 +268,16 @@ void FixSMD::smd_tether()
ftotal[0] -= fx*massfrac;
ftotal[1] -= fy*massfrac;
ftotal[2] -= fz*massfrac;
if (evflag) {
domain->unmap(x[i],image[i],unwrap);
v[0] = fx*massfrac*unwrap[0];
v[1] = fy*massfrac*unwrap[1];
v[2] = fz*massfrac*unwrap[2];
v[3] = fx*massfrac*unwrap[1];
v[4] = fx*massfrac*unwrap[2];
v[5] = fy*massfrac*unwrap[2];
v_tally(i, v);
}
}
} else {
for (int i = 0; i < nlocal; i++)
@ -270,6 +289,16 @@ void FixSMD::smd_tether()
ftotal[0] -= fx*massfrac;
ftotal[1] -= fy*massfrac;
ftotal[2] -= fz*massfrac;
if (evflag) {
domain->unmap(x[i],image[i],unwrap);
v[0] = fx*massfrac*unwrap[0];
v[1] = fy*massfrac*unwrap[1];
v[2] = fz*massfrac*unwrap[2];
v[3] = fx*massfrac*unwrap[1];
v[4] = fx*massfrac*unwrap[2];
v[5] = fy*massfrac*unwrap[2];
v_tally(i, v);
}
}
}
}