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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1360 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2008-01-09 21:56:57 +00:00
parent 6eacb0b5f9
commit b2b8adfae9
99 changed files with 487 additions and 375 deletions
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164
src/fix_shake.cpp
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@ -379,7 +379,7 @@ void FixShake::init()
SHAKE as pre-integrator constraint
------------------------------------------------------------------------- */
void FixShake::setup()
void FixShake::setup(int vflag)
{
pre_neighbor();
@ -398,14 +398,14 @@ void FixShake::setup()
if (strcmp(update->integrate_style,"verlet") == 0) {
dtv = update->dt;
dtfsq = 0.5 * update->dt * update->dt * force->ftm2v;
post_force(1);
post_force(vflag);
dtfsq = update->dt * update->dt * force->ftm2v;
} else {
dtv = step_respa[0];
dtf_innerhalf = 0.5 * step_respa[0] * force->ftm2v;
dtf_inner = dtf_innerhalf;
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
post_force_respa(1,nlevels_respa-1,0);
post_force_respa(vflag,nlevels_respa-1,0);
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
dtf_inner = step_respa[0] * force->ftm2v;
}
@ -490,7 +490,7 @@ void FixShake::pre_neighbor()
compute the force adjustment for SHAKE constraint
------------------------------------------------------------------------- */
void FixShake::post_force(int vflag_in)
void FixShake::post_force(int vflag)
{
if (update->ntimestep == next_output) stats();
@ -502,10 +502,10 @@ void FixShake::post_force(int vflag_in)
if (nprocs > 1) comm->comm_fix(this);
// zero out SHAKE contribution to virial
// virial setup
vflag = vflag_in;
if (vflag) for (int n = 0; n < 6; n++) virial[n] = 0.0;
if (vflag) v_setup(vflag);
else evflag = 0;
// loop over clusters
@ -1148,6 +1148,9 @@ void FixShake::unconstrained_update()
void FixShake::shake2(int m)
{
int nlist,list[2];
double v[6];
// local atom IDs and constraint distances
int i0 = atom->map(shake_atom[m][0]);
@ -1218,18 +1221,19 @@ void FixShake::shake2(int m)
f[i1][2] -= lamda*r01[2];
}
if (vflag) {
int factor = 0;
if (i0 < nlocal) factor++;
if (i1 < nlocal) factor++;
double rfactor = 0.5 * factor;
if (evflag) {
nlist = 0;
if (i0 < nlocal) list[nlist++] = i0;
if (i1 < nlocal) list[nlist++] = i1;
virial[0] += rfactor*lamda*r01[0]*r01[0];
virial[1] += rfactor*lamda*r01[1]*r01[1];
virial[2] += rfactor*lamda*r01[2]*r01[2];
virial[3] += rfactor*lamda*r01[0]*r01[1];
virial[4] += rfactor*lamda*r01[0]*r01[2];
virial[5] += rfactor*lamda*r01[1]*r01[2];
v[0] = lamda*r01[0]*r01[0];
v[1] = lamda*r01[1]*r01[1];
v[2] = lamda*r01[2]*r01[2];
v[3] = lamda*r01[0]*r01[1];
v[4] = lamda*r01[0]*r01[2];
v[5] = lamda*r01[1]*r01[2];
v_tally(nlist,list,2.0,v);
}
}
@ -1237,6 +1241,9 @@ void FixShake::shake2(int m)
void FixShake::shake3(int m)
{
int nlist,list[3];
double v[6];
// local atom IDs and constraint distances
int i0 = atom->map(shake_atom[m][0]);
@ -1371,26 +1378,20 @@ void FixShake::shake3(int m)
f[i2][2] -= lamda02*r02[2];
}
if (vflag) {
int factor = 0;
if (i0 < nlocal) factor++;
if (i1 < nlocal) factor++;
if (i2 < nlocal) factor++;
double rfactor = factor/3.0;
if (evflag) {
nlist = 0;
if (i0 < nlocal) list[nlist++] = i0;
if (i1 < nlocal) list[nlist++] = i1;
if (i2 < nlocal) list[nlist++] = i2;
virial[0] += rfactor*lamda01*r01[0]*r01[0];
virial[1] += rfactor*lamda01*r01[1]*r01[1];
virial[2] += rfactor*lamda01*r01[2]*r01[2];
virial[3] += rfactor*lamda01*r01[0]*r01[1];
virial[4] += rfactor*lamda01*r01[0]*r01[2];
virial[5] += rfactor*lamda01*r01[1]*r01[2];
v[0] = lamda01*r01[0]*r01[0] + lamda02*r02[0]*r02[0];
v[1] = lamda01*r01[1]*r01[1] + lamda02*r02[1]*r02[1];
v[2] = lamda01*r01[2]*r01[2] + lamda02*r02[2]*r02[2];
v[3] = lamda01*r01[0]*r01[1] + lamda02*r02[0]*r02[1];
v[4] = lamda01*r01[0]*r01[2] + lamda02*r02[0]*r02[2];
v[5] = lamda01*r01[1]*r01[2] + lamda02*r02[1]*r02[2];
virial[0] += rfactor*lamda02*r02[0]*r02[0];
virial[1] += rfactor*lamda02*r02[1]*r02[1];
virial[2] += rfactor*lamda02*r02[2]*r02[2];
virial[3] += rfactor*lamda02*r02[0]*r02[1];
virial[4] += rfactor*lamda02*r02[0]*r02[2];
virial[5] += rfactor*lamda02*r02[1]*r02[2];
v_tally(nlist,list,3.0,v);
}
}
@ -1398,6 +1399,9 @@ void FixShake::shake3(int m)
void FixShake::shake4(int m)
{
int nlist,list[4];
double v[6];
// local atom IDs and constraint distances
int i0 = atom->map(shake_atom[m][0]);
@ -1608,34 +1612,21 @@ void FixShake::shake4(int m)
f[i3][2] -= lamda03*r03[2];
}
if (vflag) {
int factor = 0;
if (i0 < nlocal) factor++;
if (i1 < nlocal) factor++;
if (i2 < nlocal) factor++;
if (i3 < nlocal) factor++;
double rfactor = 0.25*factor;
if (evflag) {
nlist = 0;
if (i0 < nlocal) list[nlist++] = i0;
if (i1 < nlocal) list[nlist++] = i1;
if (i2 < nlocal) list[nlist++] = i2;
if (i3 < nlocal) list[nlist++] = i3;
virial[0] += rfactor*lamda01*r01[0]*r01[0];
virial[1] += rfactor*lamda01*r01[1]*r01[1];
virial[2] += rfactor*lamda01*r01[2]*r01[2];
virial[3] += rfactor*lamda01*r01[0]*r01[1];
virial[4] += rfactor*lamda01*r01[0]*r01[2];
virial[5] += rfactor*lamda01*r01[1]*r01[2];
v[0] = lamda01*r01[0]*r01[0]+lamda02*r02[0]*r02[0]+lamda03*r03[0]*r03[0];
v[1] = lamda01*r01[1]*r01[1]+lamda02*r02[1]*r02[1]+lamda03*r03[1]*r03[1];
v[2] = lamda01*r01[2]*r01[2]+lamda02*r02[2]*r02[2]+lamda03*r03[2]*r03[2];
v[3] = lamda01*r01[0]*r01[1]+lamda02*r02[0]*r02[1]+lamda03*r03[0]*r03[1];
v[4] = lamda01*r01[0]*r01[2]+lamda02*r02[0]*r02[2]+lamda03*r03[0]*r03[2];
v[5] = lamda01*r01[1]*r01[2]+lamda02*r02[1]*r02[2]+lamda03*r03[1]*r03[2];
virial[0] += rfactor*lamda02*r02[0]*r02[0];
virial[1] += rfactor*lamda02*r02[1]*r02[1];
virial[2] += rfactor*lamda02*r02[2]*r02[2];
virial[3] += rfactor*lamda02*r02[0]*r02[1];
virial[4] += rfactor*lamda02*r02[0]*r02[2];
virial[5] += rfactor*lamda02*r02[1]*r02[2];
virial[0] += rfactor*lamda03*r03[0]*r03[0];
virial[1] += rfactor*lamda03*r03[1]*r03[1];
virial[2] += rfactor*lamda03*r03[2]*r03[2];
virial[3] += rfactor*lamda03*r03[0]*r03[1];
virial[4] += rfactor*lamda03*r03[0]*r03[2];
virial[5] += rfactor*lamda03*r03[1]*r03[2];
v_tally(nlist,list,4.0,v);
}
}
@ -1643,6 +1634,9 @@ void FixShake::shake4(int m)
void FixShake::shake3angle(int m)
{
int nlist,list[3];
double v[6];
// local atom IDs and constraint distances
int i0 = atom->map(shake_atom[m][0]);
@ -1845,33 +1839,20 @@ void FixShake::shake3angle(int m)
f[i2][2] -= lamda02*r02[2] + lamda12*r12[2];
}
if (vflag) {
int factor = 0;
if (i0 < nlocal) factor++;
if (i1 < nlocal) factor++;
if (i2 < nlocal) factor++;
double rfactor = factor/3.0;
if (evflag) {
nlist = 0;
if (i0 < nlocal) list[nlist++] = i0;
if (i1 < nlocal) list[nlist++] = i1;
if (i2 < nlocal) list[nlist++] = i2;
virial[0] += rfactor*lamda01*r01[0]*r01[0];
virial[1] += rfactor*lamda01*r01[1]*r01[1];
virial[2] += rfactor*lamda01*r01[2]*r01[2];
virial[3] += rfactor*lamda01*r01[0]*r01[1];
virial[4] += rfactor*lamda01*r01[0]*r01[2];
virial[5] += rfactor*lamda01*r01[1]*r01[2];
v[0] = lamda01*r01[0]*r01[0]+lamda02*r02[0]*r02[0]+lamda12*r12[0]*r12[0];
v[1] = lamda01*r01[1]*r01[1]+lamda02*r02[1]*r02[1]+lamda12*r12[1]*r12[1];
v[2] = lamda01*r01[2]*r01[2]+lamda02*r02[2]*r02[2]+lamda12*r12[2]*r12[2];
v[3] = lamda01*r01[0]*r01[1]+lamda02*r02[0]*r02[1]+lamda12*r12[0]*r12[1];
v[4] = lamda01*r01[0]*r01[2]+lamda02*r02[0]*r02[2]+lamda12*r12[0]*r12[2];
v[5] = lamda01*r01[1]*r01[2]+lamda02*r02[1]*r02[2]+lamda12*r12[1]*r12[2];
virial[0] += rfactor*lamda02*r02[0]*r02[0];
virial[1] += rfactor*lamda02*r02[1]*r02[1];
virial[2] += rfactor*lamda02*r02[2]*r02[2];
virial[3] += rfactor*lamda02*r02[0]*r02[1];
virial[4] += rfactor*lamda02*r02[0]*r02[2];
virial[5] += rfactor*lamda02*r02[1]*r02[2];
virial[0] += rfactor*lamda12*r12[0]*r12[0];
virial[1] += rfactor*lamda12*r12[1]*r12[1];
virial[2] += rfactor*lamda12*r12[2]*r12[2];
virial[3] += rfactor*lamda12*r12[0]*r12[1];
virial[4] += rfactor*lamda12*r12[0]*r12[2];
virial[5] += rfactor*lamda12*r12[1]*r12[2];
v_tally(nlist,list,3.0,v);
}
}
@ -2064,6 +2045,7 @@ double FixShake::memory_usage()
bytes += nmax*4 * sizeof(int);
bytes += nmax*3 * sizeof(int);
bytes += nmax*3 * sizeof(double);
bytes += maxvatom*6 * sizeof(double);
return bytes;
}
@ -2199,7 +2181,7 @@ int FixShake::unpack_exchange(int nlocal, double *buf)
rRESPA updating of atom coords is done with full v, but only portions of f
------------------------------------------------------------------------- */
void FixShake::post_force_respa(int vflag_in, int ilevel, int iloop)
void FixShake::post_force_respa(int vflag, int ilevel, int iloop)
{
// call stats only on outermost level
@ -2242,10 +2224,10 @@ void FixShake::post_force_respa(int vflag_in, int ilevel, int iloop)
if (nprocs > 1) comm->comm_fix(this);
// zero out SHAKE contribution to virial
// virial setup
vflag = vflag_in;
if (vflag) for (int n = 0; n < 6; n++) virial[n] = 0.0;
if (vflag) v_setup(vflag);
else evflag = 0;
// loop over clusters