Patch file for module: Abrupt AdResSΒΆ
The patch for the abrupt AdResS code is:
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--- /storage/mi/ck69giso/gromacs-5.1.5/src/gromacs/legacyheaders/update.h 2016-07-13 14:56:04.000000000 +0200
+++ /home/mi/ck69giso/gmx-515-lt/src/gromacs/legacyheaders/update.h 2018-12-03 12:07:23.228392303 +0100
@@ -102,7 +102,9 @@
t_commrec *cr, /* these shouldn't be here -- need to think about it */
t_nrnb *nrnb,
gmx_constr_t constr,
- t_idef *idef);
+ t_idef *idef,
+ t_forcerec *fr);
+
/* Return TRUE if OK, FALSE in case of Shake Error */
@@ -125,7 +127,8 @@
gmx_update_t upd,
gmx_constr_t constr,
gmx_bool bFirstHalf,
- gmx_bool bCalcVir);
+ gmx_bool bCalcVir,
+ t_forcerec *fr);
/* Return TRUE if OK, FALSE in case of Shake Error */
diff -Naur /storage/mi/ck69giso/gromacs-5.1.5/src/gromacs/mdlib/adress.c /home/mi/ck69giso/gmx-515-lt/src/gromacs/mdlib/adress.c
--- /storage/mi/ck69giso/gromacs-5.1.5/src/gromacs/mdlib/adress.c 2016-07-13 14:56:04.000000000 +0200
+++ /home/mi/ck69giso/gmx-515-lt/src/gromacs/mdlib/adress.c 2018-08-15 12:39:32.000000000 +0200
@@ -101,17 +101,17 @@
return 0;
}
/* molecule is explicit */
- else if (sqr_dl < adressr*adressr)
+ else //if (sqr_dl < adressr*adressr)
{
return 1;
}
- /* hybrid region */
+ /* hybrid region
else
- {
- dl = sqrt(sqr_dl);
- tmp = cos((dl-adressr)*M_PI/2/adressw);
- return tmp*tmp;
- }
+ {
+// dl = sqrt(sqr_dl);
+// tmp = cos((dl-adressr)*M_PI/2/adressw);
+ return 0.5;
+ } */
}
void
diff -Naur /storage/mi/ck69giso/gromacs-5.1.5/src/gromacs/mdlib/ns.c /home/mi/ck69giso/gmx-515-lt/src/gromacs/mdlib/ns.c
--- /storage/mi/ck69giso/gromacs-5.1.5/src/gromacs/mdlib/ns.c 2016-07-13 14:56:04.000000000 +0200
+++ /home/mi/ck69giso/gmx-515-lt/src/gromacs/mdlib/ns.c 2018-08-15 12:55:06.000000000 +0200
@@ -264,10 +264,12 @@
for (i = 0; i < fr->nnblists; i++)
{
nbl = &(fr->nblists[i]);
-
- if ((fr->adress_type != eAdressOff) && (i >= fr->nnblists/2))
+/* chk */
+// if ((fr->adress_type != eAdressOff) && (i >= fr->nnblists/2))
+ if ((fr->adress_type != eAdressOff))
{
- type = GMX_NBLIST_INTERACTION_ADRESS;
+ /* type = GMX_NBLIST_INTERACTION_ADRESS; */
+ type = GMX_NBLIST_INTERACTION_STANDARD;
}
init_nblist(log, &nbl->nlist_sr[eNL_VDWQQ], &nbl->nlist_lr[eNL_VDWQQ],
maxsr, maxlr, ivdw, ivdwmod, ielec, ielecmod, igeometry_def, type, bElecAndVdwSwitchDiffers);
@@ -601,11 +603,14 @@
int *cginfo;
int *type, *typeB;
real *charge, *chargeB;
+ real *wf;
real qi, qiB, qq, rlj;
gmx_bool bFreeEnergy, bFree, bFreeJ, bNotEx, *bPert;
gmx_bool bDoVdW_i, bDoCoul_i, bDoCoul_i_sol;
+ gmx_bool b_hybrid;
int iwater, jwater;
t_nblist *nlist;
+ gmx_bool bEnergyGroupCG;
/* Copy some pointers */
cginfo = fr->cginfo;
@@ -614,6 +619,7 @@
type = md->typeA;
typeB = md->typeB;
bPert = md->bPerturbed;
+ wf = md->wf;
/* Get atom range */
i0 = index[icg];
@@ -625,7 +631,7 @@
iwater = (solvent_opt != esolNO) ? GET_CGINFO_SOLOPT(cginfo[icg]) : esolNO;
bFreeEnergy = FALSE;
- if (md->nPerturbed)
+ if (md->nPerturbed )
{
/* Check if any of the particles involved are perturbed.
* If not we can do the cheaper normal put_in_list
@@ -683,6 +689,7 @@
}
if (!bFreeEnergy)
+/* if (!bFreeEnergy || (fr->adress_type != eAdressOff)) */
{
if (iwater != esolNO)
{
@@ -846,8 +853,13 @@
bDoVdW_i = (bDoVdW && bHaveVdW[type[i_atom]]);
bDoCoul_i = (bDoCoul && qi != 0);
+ /* chk */
+ bEnergyGroupCG = !egp_explicit(fr, igid);
+ /* chk */
+
if (bDoVdW_i || bDoCoul_i)
{
+
/* Loop over the j charge groups */
for (j = 0; (j < nj); j++)
{
@@ -867,7 +879,19 @@
/* Finally loop over the atoms in the j-charge group */
for (jj = jj0; jj < jj1; jj++)
{
+
bNotEx = NOTEXCL(bExcl, i, jj);
+ /* change 7.11.2017 chk*/
+ if ( fr->adress_type != eAdressOff )
+ {
+ if ( ( !bEnergyGroupCG && ( wf[i_atom] <= GMX_REAL_EPS || wf[jj] <= GMX_REAL_EPS ) ) ||
+ ( ( bEnergyGroupCG ) && ( wf[i_atom] > GMX_REAL_EPS || wf[jj] > GMX_REAL_EPS ) ))
+// abrupt-GC ( ( bEnergyGroupCG ) && ( wf[i_atom] > GMX_REAL_EPS && wf[jj] > GMX_REAL_EPS ) ))
+ {
+ continue;
+ }
+ }
+ /* change 7.11.2017 chk*/
if (bNotEx)
{
@@ -984,6 +1008,10 @@
jj1 = index[jcg+1];
/* Finally loop over the atoms in the j-charge group */
bFree = bPert[i_atom];
+
+ /* chk
+ bEnergyGroupCG = !egp_explicit(fr, igid); */
+
for (jj = jj0; (jj < jj1); jj++)
{
bFreeJ = bFree || bPert[jj];
@@ -994,6 +1022,16 @@
{
bNotEx = NOTEXCL(bExcl, i, jj);
+ /* chk
+
+ if ( ( !bEnergyGroupCG && ( wf[i_atom] <= GMX_REAL_EPS || wf[jj] <= GMX_REAL_EPS ) ) ||
+ ( ( bEnergyGroupCG ) && ( wf[i_atom] >= GMX_REAL_EPS && wf[jj] >= GMX_REAL_EPS ) )
+ )
+
+ {
+ continue;
+ } */
+
if (bNotEx)
{
if (bFreeJ)
@@ -1250,6 +1288,19 @@
* b_hybrid=true are placed into the _adress neighbour lists and
* processed by the generic AdResS kernel.
*/
+ /* change 7.11.2017 chk*/
+ /* if ( fr->adress_type != eAdressOff )
+ { */
+ if ( ( !bEnergyGroupCG && ( wf[i_atom] <= GMX_REAL_EPS || wf[jj] <= GMX_REAL_EPS ) ) ||
+ ( ( bEnergyGroupCG ) && ( wf[i_atom] > GMX_REAL_EPS || wf[jj] > GMX_REAL_EPS ) )
+// ( ( bEnergyGroupCG ) && ( wf[i_atom] > GMX_REAL_EPS && wf[jj] > GMX_REAL_EPS ) )
+ )
+
+ {
+ continue;
+ }
+ /* } */
+/* old version from normal GC-AdResS before october 7
if ( (bEnergyGroupCG &&
wf[i_atom] >= 1-GMX_REAL_EPS && wf[jj] >= 1-GMX_REAL_EPS ) ||
( !bEnergyGroupCG && wf[jj] <= GMX_REAL_EPS ) )
@@ -1259,6 +1310,7 @@
b_hybrid = !((wf[i_atom] >= 1-GMX_REAL_EPS && wf[jj] >= 1-GMX_REAL_EPS) ||
(wf[i_atom] <= GMX_REAL_EPS && wf[jj] <= GMX_REAL_EPS));
+*/
if (bNotEx)
{
@@ -1266,28 +1318,15 @@
{
if (charge[jj] != 0)
{
- if (!b_hybrid)
- {
- add_j_to_nblist(coul, jj, bLR);
- }
- else
- {
- add_j_to_nblist(coul_adress, jj, bLR);
- }
+ /* chk: removed the !b_hybrid if loops */
+ add_j_to_nblist(coul, jj, bLR);
}
}
else if (!bDoCoul_i)
{
if (bHaveVdW[type[jj]])
{
- if (!b_hybrid)
- {
add_j_to_nblist(vdw, jj, bLR);
- }
- else
- {
- add_j_to_nblist(vdw_adress, jj, bLR);
- }
}
}
else
@@ -1296,38 +1335,16 @@
{
if (charge[jj] != 0)
{
- if (!b_hybrid)
- {
add_j_to_nblist(vdwc, jj, bLR);
- }
- else
- {
- add_j_to_nblist(vdwc_adress, jj, bLR);
- }
}
else
{
- if (!b_hybrid)
- {
add_j_to_nblist(vdw, jj, bLR);
- }
- else
- {
- add_j_to_nblist(vdw_adress, jj, bLR);
- }
-
}
}
else if (charge[jj] != 0)
{
- if (!b_hybrid)
- {
add_j_to_nblist(coul, jj, bLR);
- }
- else
- {
- add_j_to_nblist(coul_adress, jj, bLR);
- }
}
}
@@ -2671,8 +2688,10 @@
rvec box_size, grid_x0, grid_x1;
int i, j, m, ngid;
real min_size, grid_dens;
+ real b_hybrid;
int nsearch;
gmx_bool bGrid;
+ gmx_bool bEnergyGroupCG;
char *ptr;
gmx_bool *i_egp_flags;
int cg_start, cg_end, start, end;
@@ -2774,8 +2793,9 @@
}
debug_gmx();
- if (fr->adress_type == eAdressOff)
- {
+/* chk */
+// if (fr->adress_type == eAdressOff)
+// {
if (!fr->ns.bCGlist)
{
put_in_list = put_in_list_at;
@@ -2784,11 +2804,12 @@
{
put_in_list = put_in_list_cg;
}
- }
- else
- {
- put_in_list = put_in_list_adress;
- }
+// }
+// else
+// {
+// put_in_list = put_in_list_adress;
+// }
+/* chk */
/* Do the core! */
if (bGrid)
diff -Naur /storage/mi/ck69giso/gromacs-5.1.5/src/gromacs/mdlib/update.cpp /home/mi/ck69giso/gmx-515-lt/src/gromacs/mdlib/update.cpp
--- /storage/mi/ck69giso/gromacs-5.1.5/src/gromacs/mdlib/update.cpp 2016-09-07 14:50:21.000000000 +0200
+++ /home/mi/ck69giso/gmx-515-lt/src/gromacs/mdlib/update.cpp 2018-12-03 12:19:21.924644082 +0100
@@ -67,6 +67,7 @@
#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxomp.h"
#include "gromacs/utility/smalloc.h"
+#include "adress.h"
/*For debugging, start at v(-dt/2) for velolcity verlet -- uncomment next line */
/*#define STARTFROMDT2*/
@@ -569,6 +570,8 @@
return upd;
}
+/* new */
+
static void do_update_sd1(gmx_stochd_t *sd,
int start, int nrend, double dt,
rvec accel[], ivec nFreeze[],
@@ -579,14 +582,28 @@
int ngtc, real ref_t[],
gmx_bool bDoConstr,
gmx_bool bFirstHalfConstr,
- gmx_int64_t step, int seed, int* gatindex)
+ gmx_int64_t step, int seed, int* gatindex, real fc, t_forcerec *fr)
{
gmx_sd_const_t *sdc;
gmx_sd_sigma_t *sig;
+
real kT;
int gf = 0, ga = 0, gt = 0;
real ism;
- int n, d;
+ int i, n, d;
+
+ int adresstype;
+ real adressr, sqr_dl, dl;
+// real adressw;
+ rvec *ref, dx, xnew;
+
+ adresstype = fr->adress_type;
+ adressr = fr->adress_ex_width;
+// adressw = fr->adress_hy_width;
+ ref = &(fr->adress_refs);
+
+ //real l2 = adressr + adressw;
+ real fc1 = fc;
sdc = sd->sdc;
sig = sd->sdsig;
@@ -621,14 +638,65 @@
gmx_rng_cycle_3gaussian_table(step, ng, seed, RND_SEED_UPDATE, rnd);
+ xnew[0] = x[n][0], xnew[1] = x[n][1], xnew[2] = x[n][2];
+ rvec_sub((*ref), xnew, dx);
+ sqr_dl = 0.0;
+ switch (adresstype)
+ {
+ case eAdressXSplit:
+ /* plane through center of ref, varies in x direction */
+ sqr_dl = dx[0]*dx[0];
+ break;
+ case eAdressSphere:
+ /* point at center of ref, assuming cubic geometry */
+ // sqr_dl = 0.0;
+ for (i = 0; i < 3; i++)
+ {
+ sqr_dl += dx[i]*dx[i];
+ }
+ break;
+ }
+ /* Don't thermostat the explicit region */
+ dl = sqrt(sqr_dl);
+
+ if (dl < adressr)
+ {
+ for (d = 0; d < DIM; d++)
+ {
+ if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d])
+ {
+// real sd_V;
+ real vn, fn;
+ fn = f[n][d];
+ vn = v[n][d] + (invmass[n]*fn + accel[ga][d])*dt;
+ /* Here we include half of the friction+noise
+ * update of v into the integration of x.
+ */
+ xprime[n][d] = x[n][d] + 0.5*(vn + v[n][d])*dt;
+ }
+ else
+ {
+ v[n][d] = 0.0;
+ xprime[n][d] = x[n][d];
+ }
+ }
+ continue;
+ }
+
for (d = 0; d < DIM; d++)
{
if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d])
{
- real sd_V, vn;
+ real sd_V, vn, fn;
+ fn = f[n][d];
+ if (fabs(fn)>fc)
+ {
+// printf("SD (I) force-cap %e\n", fn);
+ fn = fc1*fn/fabs(fn);
+ }
sd_V = ism*sig[gt].V*rnd[d];
- vn = v[n][d] + (invmass[n]*f[n][d] + accel[ga][d])*dt;
+ vn = v[n][d] + (invmass[n]*fn + accel[ga][d])*dt;
v[n][d] = vn*sdc[gt].em + sd_V;
/* Here we include half of the friction+noise
* update of v into the integration of x.
@@ -663,12 +731,39 @@
{
ga = cACC[n];
}
+
+ xnew[0] = x[n][0], xnew[1] = x[n][1], xnew[2] = x[n][2];
+ rvec_sub((*ref), xnew, dx);
+ sqr_dl = 0.0;
+ switch (adresstype)
+ {
+ case eAdressXSplit:
+ /* plane through center of ref, varies in x direction */
+ sqr_dl = dx[0]*dx[0];
+ break;
+ case eAdressSphere:
+ /* point at center of ref, assuming cubic geometry */
+ // sqr_dl = 0.0;
+ for (i = 0; i < 3; i++)
+ {
+ sqr_dl += dx[i]*dx[i];
+ }
+ break;
+ }
+ /* Don't thermostat the explicit region */
+ dl = sqrt(sqr_dl);
+ if (dl < adressr)
+ {
for (d = 0; d < DIM; d++)
{
if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d])
{
- v[n][d] = v[n][d] + (im*f[n][d] + accel[ga][d])*dt;
+
+ real fn;
+ fn = f[n][d];
+
+ v[n][d] = v[n][d] + (im*fn + accel[ga][d])*dt;
xprime[n][d] = x[n][d] + v[n][d]*dt;
}
else
@@ -677,6 +772,31 @@
xprime[n][d] = x[n][d];
}
}
+ continue;
+ }
+ for (d = 0; d < DIM; d++)
+ {
+ if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d])
+ {
+
+ real fn;
+ fn = f[n][d];
+ if (fabs(fn)>fc)
+ {
+ // printf("SD (II) force-cap %e\n", fn);
+ fn = fc*fn/fabs(fn);
+ }
+
+ v[n][d] = v[n][d] + (im*fn + accel[ga][d])*dt;
+ // v[n][d] = v[n][d] + (im*f[n][d] + accel[ga][d])*dt;
+ xprime[n][d] = x[n][d] + v[n][d]*dt;
+ }
+ else
+ {
+ v[n][d] = 0.0;
+ xprime[n][d] = x[n][d];
+ }
+ }
}
}
else
@@ -697,8 +817,45 @@
gt = cTC[n];
}
+ xnew[0] = x[n][0], xnew[1] = x[n][1], xnew[2] = x[n][2];
+ rvec_sub((*ref), xnew, dx);
+ sqr_dl = 0.0;
+ switch (adresstype)
+ {
+ case eAdressXSplit:
+ /* plane through center of ref, varies in x direction */
+ sqr_dl = dx[0]*dx[0];
+ break;
+ case eAdressSphere:
+ /* point at center of ref, assuming cubic geometry */
+ // sqr_dl = 0.0;
+ for (i = 0; i < 3; i++)
+ {
+ sqr_dl += dx[i]*dx[i];
+ }
+ break;
+ }
gmx_rng_cycle_3gaussian_table(step, ng, seed, RND_SEED_UPDATE, rnd);
+ /* Don't thermostat the explicit region */
+
+ dl = sqrt(sqr_dl);
+ // real l2 = adressr+adressw;
+
+ if (dl < adressr)
+ {
+ for (d = 0; d < DIM; d++)
+ {
+ if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d])
+ {
+ real vn;
+
+ vn = v[n][d];
+ xprime[n][d] = xprime[n][d] + 0.5*(v[n][d] - vn)*dt;
+ }
+ }
+ continue;
+ }
for (d = 0; d < DIM; d++)
{
if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d])
@@ -1523,7 +1680,8 @@
gmx_update_t upd,
gmx_constr_t constr,
gmx_bool bFirstHalf,
- gmx_bool bCalcVir)
+ gmx_bool bCalcVir,
+ t_forcerec *fr)
{
gmx_bool bLastStep, bLog = FALSE, bEner = FALSE, bDoConstr = FALSE;
double dt;
@@ -1644,6 +1802,8 @@
end_th = start + ((nrend-start)*(th+1))/nth;
/* The second part of the SD integration */
+ if (inputrec->bAdress)
+ {
do_update_sd1(upd->sd,
start_th, end_th, dt,
inputrec->opts.acc, inputrec->opts.nFreeze,
@@ -1653,7 +1813,23 @@
inputrec->opts.ngtc, inputrec->opts.ref_t,
bDoConstr, FALSE,
step, inputrec->ld_seed,
- DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
+ DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL,
+ inputrec->adress->ex_forcecap, fr);
+ }
+ else
+ {
+ do_update_sd1(upd->sd,
+ start_th, end_th, dt,
+ inputrec->opts.acc, inputrec->opts.nFreeze,
+ md->invmass, md->ptype,
+ md->cFREEZE, md->cACC, md->cTC,
+ state->x, xprime, state->v, force,
+ inputrec->opts.ngtc, inputrec->opts.ref_t,
+ bDoConstr, FALSE,
+ step, inputrec->ld_seed,
+ DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL,
+ 5000., fr);
+ }
}
inc_nrnb(nrnb, eNR_UPDATE, homenr);
wallcycle_stop(wcycle, ewcUPDATE);
@@ -1912,7 +2088,8 @@
t_commrec *cr, /* these shouldn't be here -- need to think about it */
t_nrnb *nrnb,
gmx_constr_t constr,
- t_idef *idef)
+ t_idef *idef,
+ t_forcerec *fr)
{
gmx_bool bNH, bPR, bDoConstr = FALSE;
double dt, alpha;
@@ -2031,6 +2208,21 @@
break;
case (eiSD1):
/* With constraints, the SD1 update is done in 2 parts */
+ if (inputrec->bAdress)
+ {
+ do_update_sd1(upd->sd,
+ start_th, end_th, dt,
+ inputrec->opts.acc, inputrec->opts.nFreeze,
+ md->invmass, md->ptype,
+ md->cFREEZE, md->cACC, md->cTC,
+ state->x, xprime, state->v, force,
+ inputrec->opts.ngtc, inputrec->opts.ref_t,
+ bDoConstr, TRUE,
+ step, inputrec->ld_seed, DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL,
+ inputrec->adress->ex_forcecap, fr);
+ }
+ else
+ {
do_update_sd1(upd->sd,
start_th, end_th, dt,
inputrec->opts.acc, inputrec->opts.nFreeze,
@@ -2039,7 +2231,9 @@
state->x, xprime, state->v, force,
inputrec->opts.ngtc, inputrec->opts.ref_t,
bDoConstr, TRUE,
- step, inputrec->ld_seed, DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
+ step, inputrec->ld_seed, DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL,
+ 5000., fr);
+ }
break;
case (eiSD2):
/* The SD2 update is always done in 2 parts,
diff -Naur /storage/mi/ck69giso/gromacs-5.1.5/src/programs/mdrun/md.cpp /home/mi/ck69giso/gmx-515-lt/src/programs/mdrun/md.cpp
--- /storage/mi/ck69giso/gromacs-5.1.5/src/programs/mdrun/md.cpp 2017-12-21 10:16:18.000000000 +0100
+++ /home/mi/ck69giso/gmx-515-lt/src/programs/mdrun/md.cpp 2018-12-03 12:14:02.874757865 +0100
@@ -1124,7 +1124,7 @@
update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC,
f, bUpdateDoLR, fr->f_twin, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
ekind, M, upd, bInitStep, etrtVELOCITY1,
- cr, nrnb, constr, &top->idef);
+ cr, nrnb, constr, &top->idef, fr);
if (!bRerunMD || rerun_fr.bV || bForceUpdate) /* Why is rerun_fr.bV here? Unclear. */
{
@@ -1133,7 +1133,7 @@
state, fr->bMolPBC, graph, f,
&top->idef, shake_vir,
cr, nrnb, wcycle, upd, constr,
- TRUE, bCalcVir);
+ TRUE, bCalcVir, fr);
wallcycle_start(wcycle, ewcUPDATE);
if (bCalcVir && bUpdateDoLR && ir->nstcalclr > 1)
{
@@ -1376,7 +1376,7 @@
state, fr->bMolPBC, graph, f,
&top->idef, tmp_vir,
cr, nrnb, wcycle, upd, constr,
- TRUE, bCalcVir);
+ TRUE, bCalcVir, fr);
}
}
/* ######### START SECOND UPDATE STEP ################# */
@@ -1416,7 +1416,7 @@
update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
bUpdateDoLR, fr->f_twin, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
ekind, M, upd, FALSE, etrtVELOCITY2,
- cr, nrnb, constr, &top->idef);
+ cr, nrnb, constr, &top->idef, fr);
}
/* Above, initialize just copies ekinh into ekin,
@@ -1438,14 +1438,14 @@
update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
bUpdateDoLR, fr->f_twin, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
- ekind, M, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef);
+ ekind, M, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef, fr);
wallcycle_stop(wcycle, ewcUPDATE);
update_constraints(fplog, step, &dvdl_constr, ir, mdatoms, state,
fr->bMolPBC, graph, f,
&top->idef, shake_vir,
cr, nrnb, wcycle, upd, constr,
- FALSE, bCalcVir);
+ FALSE, bCalcVir, fr);
if (bCalcVir && bUpdateDoLR && ir->nstcalclr > 1)
{
@@ -1472,7 +1472,7 @@
update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
bUpdateDoLR, fr->f_twin, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
- ekind, M, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef);
+ ekind, M, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef, fr);
wallcycle_stop(wcycle, ewcUPDATE);
/* do we need an extra constraint here? just need to copy out of state->v to upd->xp? */
@@ -1484,7 +1484,7 @@
state, fr->bMolPBC, graph, f,
&top->idef, tmp_vir,
cr, nrnb, wcycle, upd, NULL,
- FALSE, bCalcVir);
+ FALSE, bCalcVir, fr);
}
if (bVV)
{
|