void reset_x_ndim(int ndim,int ncm,atom_id ind_cm[],
int nreset,atom_id *ind_reset,rvec x[],real mass[])
{
int i,m,ai;
rvec xcm;
real tm,mm;
tm=0.0;
clear_rvec(xcm);
for(i=0; i<ncm; i++) {
ai=ind_cm[i];
mm=mass[ai];
for(m=0; m<ndim; m++)
xcm[m]+=mm*x[ai][m];
tm+=mm;
}
for(m=0; m<ndim; m++)
xcm[m]/=tm;
if (ind_reset)
for(i=0; i<nreset; i++)
rvec_dec(x[ind_reset[i]],xcm);
else
for(i=0; i<nreset; i++)
rvec_dec(x[i],xcm);
}
void reset_x_ndim(int ndim,int ncm,const atom_id *ind_cm,
int nreset,const atom_id *ind_reset,
rvec x[],const real mass[])
{
int i,m,ai;
rvec xcm;
real tm,mm;
if (ndim>DIM)
{
gmx_incons("More than 3 dimensions not supported.");
}
tm = 0.0;
clear_rvec(xcm);
if (ind_cm != NULL)
{
for(i=0; i<ncm; i++)
{
ai = ind_cm[i];
mm = mass[ai];
for(m=0; m<ndim; m++)
{
xcm[m] += mm*x[ai][m];
}
tm += mm;
}
}
else
{
for(i=0; i<ncm; i++)
{
mm = mass[i];
for(m=0; m<ndim; m++)
{
xcm[m] += mm*x[i][m];
}
tm += mm;
}
}
for(m=0; m<ndim; m++)
{
xcm[m] /= tm;
}
if (ind_reset != NULL)
{
for(i=0; i<nreset; i++)
{
rvec_dec(x[ind_reset[i]],xcm);
}
}
else
{
for(i=0; i<nreset; i++)
{
rvec_dec(x[i],xcm);
}
}
}
static void calc_axes(rvec x[],t_atom atom[],int gnx[],atom_id *index[],
gmx_bool bRot,t_bundle *bun)
{
int end,i,div,d;
real *mtot,m;
rvec axis[MAX_ENDS],cent;
snew(mtot,bun->n);
for(end=0; end<bun->nend; end++) {
for(i=0; i<bun->n; i++) {
clear_rvec(bun->end[end][i]);
mtot[i] = 0;
}
div = gnx[end]/bun->n;
for(i=0; i<gnx[end]; i++) {
m = atom[index[end][i]].m;
for(d=0; d<DIM; d++)
bun->end[end][i/div][d] += m*x[index[end][i]][d];
mtot[i/div] += m;
}
clear_rvec(axis[end]);
for(i=0; i<bun->n; i++) {
svmul(1.0/mtot[i],bun->end[end][i],bun->end[end][i]);
rvec_inc(axis[end],bun->end[end][i]);
}
svmul(1.0/bun->n,axis[end],axis[end]);
}
sfree(mtot);
rvec_add(axis[0],axis[1],cent);
svmul(0.5,cent,cent);
/* center the bundle on the origin */
for(end=0; end<bun->nend; end++) {
rvec_dec(axis[end],cent);
for(i=0; i<bun->n; i++)
rvec_dec(bun->end[end][i],cent);
}
if (bRot) {
/* rotate the axis parallel to the z-axis */
rotate_ends(bun,axis[0],YY,ZZ);
rotate_ends(bun,axis[0],XX,ZZ);
}
for(i=0; i<bun->n; i++) {
rvec_add(bun->end[0][i],bun->end[1][i],bun->mid[i]);
svmul(0.5,bun->mid[i],bun->mid[i]);
rvec_sub(bun->end[0][i],bun->end[1][i],bun->dir[i]);
bun->len[i] = norm(bun->dir[i]);
unitv(bun->dir[i],bun->dir[i]);
}
}
/* prepare the coordinates by removing periodic boundary crossings.
gnx = the number of atoms/molecules
index = the indices
xcur = the current coordinates
xprev = the previous coordinates
box = the box matrix */
static void prep_data(gmx_bool bMol,int gnx,atom_id index[],
rvec xcur[],rvec xprev[],matrix box)
{
int i,m,ind;
rvec hbox;
/* Remove periodicity */
for(m=0; (m<DIM); m++)
hbox[m]=0.5*box[m][m];
for(i=0; (i<gnx); i++) {
if (bMol)
ind = i;
else
ind = index[i];
for(m=DIM-1; m>=0; m--)
{
while(xcur[ind][m]-xprev[ind][m] <= -hbox[m])
rvec_inc(xcur[ind],box[m]);
while(xcur[ind][m]-xprev[ind][m] > hbox[m])
rvec_dec(xcur[ind],box[m]);
}
}
}
static void center_coords(t_atoms *atoms, matrix box, rvec x0[], int axis)
{
int i, m;
real tmass, mm;
rvec com, shift, box_center;
tmass = 0;
clear_rvec(com);
for (i = 0; (i < atoms->nr); i++)
{
mm = atoms->atom[i].m;
tmass += mm;
for (m = 0; (m < DIM); m++)
{
com[m] += mm*x0[i][m];
}
}
for (m = 0; (m < DIM); m++)
{
com[m] /= tmass;
}
calc_box_center(ecenterDEF, box, box_center);
rvec_sub(box_center, com, shift);
shift[axis] -= box_center[axis];
for (i = 0; (i < atoms->nr); i++)
{
rvec_dec(x0[i], shift);
}
}
void do_stopcm_grp(FILE *fp,int start,int homenr,unsigned short *group_id,
rvec x[],rvec v[],t_vcm *vcm)
{
int i,g,m;
real tm,tm_1;
rvec dv,dx;
if (vcm->mode != ecmNO) {
/* Subtract linear momentum */
g = 0;
switch (vcm->ndim) {
case 1:
for(i=start; (i<start+homenr); i++) {
if (group_id)
g = group_id[i];
v[i][XX] -= vcm->group_v[g][XX];
}
break;
case 2:
for(i=start; (i<start+homenr); i++) {
if (group_id)
g = group_id[i];
v[i][XX] -= vcm->group_v[g][XX];
v[i][YY] -= vcm->group_v[g][YY];
}
break;
case 3:
for(i=start; (i<start+homenr); i++) {
if (group_id)
g = group_id[i];
rvec_dec(v[i],vcm->group_v[g]);
}
break;
}
if (vcm->mode == ecmANGULAR) {
/* Subtract angular momentum */
for(i=start; (i<start+homenr); i++) {
if (group_id)
g = group_id[i];
/* Compute the correction to the velocity for each atom */
rvec_sub(x[i],vcm->group_x[g],dx);
cprod(vcm->group_w[g],dx,dv);
rvec_dec(v[i],dv);
}
}
}
}
static void my_sub_xcm(int nbb,atom_id bbind[],rvec x[],rvec xcm)
{
int i,ai;
for(i=0; (i<nbb); i++) {
ai=bbind[i];
rvec_dec(x[ai],xcm);
}
}
real sub_xcm(rvec x[], int gnx, atom_id *index, t_atom atom[], rvec xcm,
gmx_bool bQ)
{
int i, ii;
real tm;
tm = calc_xcm(x, gnx, index, atom, xcm, bQ);
for (i = 0; (i < gnx); i++)
{
ii = index ? index[i] : i;
rvec_dec(x[ii], xcm);
}
return tm;
}
static void center_molecule(int atomCount, rvec x[])
{
rvec center;
clear_rvec(center);
for (int i = 0; i < atomCount; ++i)
{
rvec_inc(center, x[i]);
}
svmul(1.0/atomCount, center, center);
for (int i = 0; i < atomCount; ++i)
{
rvec_dec(x[i], center);
}
}
static int correct_box_elem(FILE *fplog, int step, tensor box, int v, int d)
{
int shift, maxshift = 10;
shift = 0;
/* correct elem d of vector v with vector d */
while (box[v][d] > BOX_MARGIN_CORRECT*0.5*box[d][d])
{
if (fplog)
{
fprintf(fplog, "Step %d: correcting invalid box:\n", step);
pr_rvecs(fplog, 0, "old box", box, DIM);
}
rvec_dec(box[v], box[d]);
shift--;
if (fplog)
{
pr_rvecs(fplog, 0, "new box", box, DIM);
}
if (shift <= -maxshift)
{
gmx_fatal(FARGS,
"Box was shifted at least %d times. Please see log-file.",
maxshift);
}
}
while (box[v][d] < -BOX_MARGIN_CORRECT*0.5*box[d][d])
{
if (fplog)
{
fprintf(fplog, "Step %d: correcting invalid box:\n", step);
pr_rvecs(fplog, 0, "old box", box, DIM);
}
rvec_inc(box[v], box[d]);
shift++;
if (fplog)
{
pr_rvecs(fplog, 0, "new box", box, DIM);
}
if (shift >= maxshift)
{
gmx_fatal(FARGS,
"Box was shifted at least %d times. Please see log-file.",
maxshift);
}
}
return shift;
}
void
BoxDeformation::apply(ArrayRef<RVec> x,
matrix box,
int64_t step)
{
matrix updatedBox, invbox, mu;
double elapsedTime = (step + 1 - initialStep_) * timeStep_;
copy_mat(box, updatedBox);
for (int i = 0; i < DIM; i++)
{
for (int j = 0; j < DIM; j++)
{
if (deformationTensor_[i][j] != 0)
{
updatedBox[i][j] =
referenceBox_[i][j] + elapsedTime * deformationTensor_[i][j];
}
}
}
/* We correct the off-diagonal elements,
* which can grow indefinitely during shearing,
* so the shifts do not get messed up.
*/
for (int i = 1; i < DIM; i++)
{
for (int j = i-1; j >= 0; j--)
{
while (updatedBox[i][j] - box[i][j] > 0.5 * updatedBox[j][j])
{
rvec_dec(updatedBox[i], updatedBox[j]);
}
while (updatedBox[i][j] - box[i][j] < -0.5 * updatedBox[j][j])
{
rvec_inc(updatedBox[i], updatedBox[j]);
}
}
}
invertBoxMatrix(box, invbox);
// Return the updated box
copy_mat(updatedBox, box);
mmul_ur0(box, invbox, mu);
for (auto &thisX : x)
{
thisX[XX] = mu[XX][XX]*thisX[XX] + mu[YY][XX]*thisX[YY] + mu[ZZ][XX]*thisX[ZZ];
thisX[YY] = mu[YY][YY]*thisX[YY] + mu[ZZ][YY]*thisX[ZZ];
thisX[ZZ] = mu[ZZ][ZZ]*thisX[ZZ];
}
}
void print_constraint(t_pull *pull, rvec *f, int step, matrix box, int niter)
{
int i,ii,m;
rvec tmp,tmp2,tmp3;
for (i=0;i<pull->pull.n;i++) {
if (pull->bCyl)
rvec_sub(pull->pull.x_con[i],pull->dyna.x_con[i],tmp);
else
rvec_sub(pull->pull.x_con[i],pull->ref.x_con[0],tmp);
for (m=DIM-1; m>=0; m--) {
if (tmp[m] < -0.5*box[m][m]) rvec_inc(tmp,box[m]);
if (tmp[m] > 0.5*box[m][m]) rvec_dec(tmp,box[m]);
tmp[m] *= pull->dims[m];
}
if (pull->bVerbose)
fprintf(pull->out,"%d:%d ds:%e f:%e n:%d\n", step,i,norm(tmp),
pull->pull.f[i][ZZ],niter);
else
fprintf(pull->out,"%e ",pull->pull.f[i][ZZ]);
}
if (!pull->bVerbose)
fprintf(pull->out,"\n");
/* DEBUG */ /* this code doesn't correct for pbc, needs improvement */
if (pull->bVerbose) {
for (i=0;i<pull->pull.n;i++) {
if (pull->bCyl)
fprintf(pull->out,"eConstraint: step %d. Refgroup = dynamic (%f,%f\n"
"Group %d (%s): ref. dist = %8.3f, unconstr. dist = %8.3f"
" con. dist = %8.3f f_i = %8.3f\n", step, pull->r,pull->rc,
i,pull->pull.grps[i],
pull->dyna.x_ref[i][ZZ]-pull->pull.x_ref[i][ZZ],
pull->dyna.x_unc[i][ZZ]-pull->pull.x_unc[i][ZZ],
pull->dyna.x_con[i][ZZ]-pull->pull.x_con[i][ZZ],
pull->pull.f[i][ZZ]);
else {
rvec_sub(pull->ref.x_ref[0],pull->pull.x_ref[i],tmp);
rvec_sub(pull->ref.x_unc[0],pull->pull.x_unc[i],tmp2);
rvec_sub(pull->ref.x_con[0],pull->pull.x_con[i],tmp3);
fprintf(stderr,"grp %d:ref (%8.3f,%8.3f,%8.3f) unc(%8.3f%8.3f%8.3f\n"
"con (%8.3f%8.3f%8.3f)\n",i, tmp[0],tmp[1],tmp[2],
tmp2[0],tmp2[1],tmp2[2],tmp3[0],tmp3[1],tmp3[2]);
}
}
} /* END DEBUG */
}
/* prepare the coordinates by removing periodic boundary crossings.
gnx = the number of atoms/molecules
index = the indices
xcur = the current coordinates
xprev = the previous coordinates
box = the box matrix */
static void prep_data(gmx_bool bMol, int gnx, int index[],
rvec xcur[], rvec xprev[], matrix box)
{
int i, m, ind;
rvec hbox;
/* Remove periodicity */
for (m = 0; (m < DIM); m++)
{
hbox[m] = 0.5*box[m][m];
}
for (i = 0; (i < gnx); i++)
{
if (bMol)
{
ind = i;
}
else
{
ind = index[i];
}
for (m = DIM-1; m >= 0; m--)
{
if (hbox[m] == 0)
{
continue;
}
while (xcur[ind][m]-xprev[ind][m] <= -hbox[m])
{
rvec_inc(xcur[ind], box[m]);
}
while (xcur[ind][m]-xprev[ind][m] > hbox[m])
{
rvec_dec(xcur[ind], box[m]);
}
}
}
}
void correct_t0_pbc(t_pull *pull, rvec x[], t_mdatoms *md, matrix box) {
int i,ii,j,m;
real tm;
rvec com,dx;
/* loop over all atoms in index for group i. Check if they moved
more than half a box with respect to xp. If so add/subtract a box
from x0. Copy x to xp.
*/
for (i=0;i<pull->ref.ngx[0];i++) {
ii = pull->ref.idx[0][i];
/* correct for jumps across the box */
rvec_sub(x[ii],pull->ref.xp[0][i],dx);
for (m=DIM-1; m>=0; m--) {
if (dx[m] < -0.5*box[m][m]) {
rvec_inc(dx,box[m]);
if (pull->bVerbose && fabs(pull->dims[m])>GMX_REAL_MIN)
fprintf(stderr,"Jumped +box: nr %d dir: %d old:%8.3f\n",ii,m,
pull->ref.x0[0][i][m]);
}
if (dx[m] > 0.5*box[m][m]) {
rvec_dec(dx,box[m]);
if (pull->bVerbose && fabs(pull->dims[m])>GMX_REAL_MIN)
fprintf(stderr,"Jumped -box: nr %d dir: %d old:%8.3f\n",ii,m,
pull->ref.x0[0][i][m]);
}
pull->ref.x0[0][i][m] += dx[m];
pull->ref.xp[0][i][m] = x[ii][m];
}
}
tm = calc_com2(pull->ref.x0[0],pull->ref.ngx[0],pull->ref.idx[0],
md,com,box);
if (pull->bVerbose)
fprintf(stderr,"correct_t0: Group %s: mass:%8.3f com:%8.3f%8.3f%8.3f\n",
pull->ref.grps[0],tm,com[0],com[1],com[2]);
}
/* calculates com of all atoms in x[], *index has their index numbers
to get the masses from atom[] */
real calc_com2(rvec x[],int gnx,atom_id *index,t_mdatoms *md,rvec com,
matrix box)
{
int i,ii,m;
real m0,tm;
clear_rvec(com);
tm=0;
for(i=0; (i<gnx); i++) {
ii=index[i];
m0=md->massT[ii];
tm+=m0;
for(m=0; (m<DIM); m++)
com[m]+=m0*x[i][m];
}
svmul(1/tm,com,com);
for(m=DIM-1; m>=0; m--) {
/* next two lines used to be commented out */
if (com[m] < 0 ) rvec_inc(com,box[m]);
if (com[m] > box[m][m]) rvec_dec(com,box[m]);
}
return tm;
}
void calc_rm_cm(int isize, atom_id index[], t_atoms *atoms, rvec x[], rvec xcm)
{
int i, d;
real tm, m;
/* calculate and remove center of mass of reference structure */
tm = 0;
clear_rvec(xcm);
for (i = 0; i < isize; i++)
{
m = atoms->atom[index[i]].m;
for (d = 0; d < DIM; d++)
{
xcm[d] += m*x[index[i]][d];
}
tm += m;
}
svmul(1/tm, xcm, xcm);
for (i = 0; i < atoms->nr; i++)
{
rvec_dec(x[i], xcm);
}
}
void orient_princ(t_atoms *atoms, int isize, atom_id *index,
int natoms, rvec x[], rvec *v, rvec d)
{
int i, m;
rvec xcm, prcomp;
matrix trans;
calc_xcm(x, isize, index, atoms->atom, xcm, FALSE);
for (i = 0; i < natoms; i++)
{
rvec_dec(x[i], xcm);
}
principal_comp(isize, index, atoms->atom, x, trans, prcomp);
if (d)
{
copy_rvec(prcomp, d);
}
/* Check whether this trans matrix mirrors the molecule */
if (det(trans) < 0)
{
for (m = 0; (m < DIM); m++)
{
trans[ZZ][m] = -trans[ZZ][m];
}
}
rotate_atoms(natoms, NULL, x, trans);
if (v)
{
rotate_atoms(natoms, NULL, v, trans);
}
for (i = 0; i < natoms; i++)
{
rvec_inc(x[i], xcm);
}
}
void center_coords(t_atoms *atoms, atom_id *index_center, int ncenter,
matrix box, rvec x0[])
{
int i, k, m;
real tmass, mm;
rvec com, shift, box_center;
tmass = 0;
clear_rvec(com);
for (k = 0; (k < ncenter); k++)
{
i = index_center[k];
if (i >= atoms->nr)
{
gmx_fatal(FARGS, "Index %d refers to atom %d, which is larger than natoms (%d).",
k+1, i+1, atoms->nr);
}
mm = atoms->atom[i].m;
tmass += mm;
for (m = 0; (m < DIM); m++)
{
com[m] += mm*x0[i][m];
}
}
for (m = 0; (m < DIM); m++)
{
com[m] /= tmass;
}
calc_box_center(ecenterDEF, box, box_center);
rvec_sub(box_center, com, shift);
/* Important - while the center was calculated based on a group, we should move all atoms */
for (i = 0; (i < atoms->nr); i++)
{
rvec_dec(x0[i], shift);
}
}
int gmx_editconf(int argc, char *argv[])
{
const char
*desc[] =
{
"editconf converts generic structure format to [TT].gro[tt], [TT].g96[tt]",
"or [TT].pdb[tt].",
"[PAR]",
"The box can be modified with options [TT]-box[tt], [TT]-d[tt] and",
"[TT]-angles[tt]. Both [TT]-box[tt] and [TT]-d[tt]",
"will center the system in the box, unless [TT]-noc[tt] is used.",
"[PAR]",
"Option [TT]-bt[tt] determines the box type: [TT]triclinic[tt] is a",
"triclinic box, [TT]cubic[tt] is a rectangular box with all sides equal",
"[TT]dodecahedron[tt] represents a rhombic dodecahedron and",
"[TT]octahedron[tt] is a truncated octahedron.",
"The last two are special cases of a triclinic box.",
"The length of the three box vectors of the truncated octahedron is the",
"shortest distance between two opposite hexagons.",
"The volume of a dodecahedron is 0.71 and that of a truncated octahedron",
"is 0.77 of that of a cubic box with the same periodic image distance.",
"[PAR]",
"Option [TT]-box[tt] requires only",
"one value for a cubic box, dodecahedron and a truncated octahedron.",
"[PAR]",
"With [TT]-d[tt] and a [TT]triclinic[tt] box the size of the system in the x, y",
"and z directions is used. With [TT]-d[tt] and [TT]cubic[tt],",
"[TT]dodecahedron[tt] or [TT]octahedron[tt] boxes, the dimensions are set",
"to the diameter of the system (largest distance between atoms) plus twice",
"the specified distance.",
"[PAR]",
"Option [TT]-angles[tt] is only meaningful with option [TT]-box[tt] and",
"a triclinic box and can not be used with option [TT]-d[tt].",
"[PAR]",
"When [TT]-n[tt] or [TT]-ndef[tt] is set, a group",
"can be selected for calculating the size and the geometric center,",
"otherwise the whole system is used.",
"[PAR]",
"[TT]-rotate[tt] rotates the coordinates and velocities.",
"[PAR]",
"[TT]-princ[tt] aligns the principal axes of the system along the",
"coordinate axes, this may allow you to decrease the box volume,",
"but beware that molecules can rotate significantly in a nanosecond.",
"[PAR]",
"Scaling is applied before any of the other operations are",
"performed. Boxes and coordinates can be scaled to give a certain density (option",
"[TT]-density[tt]). Note that this may be inaccurate in case a gro",
"file is given as input. A special feature of the scaling option, when the",
"factor -1 is given in one dimension, one obtains a mirror image,",
"mirrored in one of the plains, when one uses -1 in three dimensions",
"a point-mirror image is obtained.[PAR]",
"Groups are selected after all operations have been applied.[PAR]",
"Periodicity can be removed in a crude manner.",
"It is important that the box sizes at the bottom of your input file",
"are correct when the periodicity is to be removed.",
"[PAR]",
"When writing [TT].pdb[tt] files, B-factors can be",
"added with the [TT]-bf[tt] option. B-factors are read",
"from a file with with following format: first line states number of",
"entries in the file, next lines state an index",
"followed by a B-factor. The B-factors will be attached per residue",
"unless an index is larger than the number of residues or unless the",
"[TT]-atom[tt] option is set. Obviously, any type of numeric data can",
"be added instead of B-factors. [TT]-legend[tt] will produce",
"a row of CA atoms with B-factors ranging from the minimum to the",
"maximum value found, effectively making a legend for viewing.",
"[PAR]",
"With the option -mead a special pdb (pqr) file for the MEAD electrostatics",
"program (Poisson-Boltzmann solver) can be made. A further prerequisite",
"is that the input file is a run input file.",
"The B-factor field is then filled with the Van der Waals radius",
"of the atoms while the occupancy field will hold the charge.",
"[PAR]",
"The option -grasp is similar, but it puts the charges in the B-factor",
"and the radius in the occupancy.",
"[PAR]",
"Option [TT]-align[tt] allows alignment",
"of the principal axis of a specified group against the given vector, ",
"with an optional center of rotation specified by [TT]-aligncenter[tt].",
"[PAR]",
"Finally with option [TT]-label[tt] editconf can add a chain identifier",
"to a pdb file, which can be useful for analysis with e.g. rasmol.",
"[PAR]",
"To convert a truncated octrahedron file produced by a package which uses",
"a cubic box with the corners cut off (such as Gromos) use:[BR]",
"[TT]editconf -f <in> -rotate 0 45 35.264 -bt o -box <veclen> -o <out>[tt][BR]",
"where [TT]veclen[tt] is the size of the cubic box times sqrt(3)/2." };
const char *bugs[] =
{
"For complex molecules, the periodicity removal routine may break down, ",
"in that case you can use trjconv." };
static real dist = 0.0, rbox = 0.0, to_diam = 0.0;
static gmx_bool bNDEF = FALSE, bRMPBC = FALSE, bCenter = FALSE, bReadVDW =
FALSE, bCONECT = FALSE;
static gmx_bool peratom = FALSE, bLegend = FALSE, bOrient = FALSE, bMead =
FALSE, bGrasp = FALSE, bSig56 = FALSE;
static rvec scale =
{ 1, 1, 1 }, newbox =
{ 0, 0, 0 }, newang =
{ 90, 90, 90 };
static real rho = 1000.0, rvdw = 0.12;
static rvec center =
{ 0, 0, 0 }, translation =
{ 0, 0, 0 }, rotangles =
{ 0, 0, 0 }, aligncenter =
{ 0, 0, 0 }, targetvec =
{ 0, 0, 0 };
static const char *btype[] =
{ NULL, "triclinic", "cubic", "dodecahedron", "octahedron", NULL },
*label = "A";
static rvec visbox =
{ 0, 0, 0 };
t_pargs
pa[] =
{
{ "-ndef", FALSE, etBOOL,
{ &bNDEF }, "Choose output from default index groups" },
{ "-visbox", FALSE, etRVEC,
{ visbox },
"HIDDENVisualize a grid of boxes, -1 visualizes the 14 box images" },
{ "-bt", FALSE, etENUM,
{ btype }, "Box type for -box and -d" },
{ "-box", FALSE, etRVEC,
{ newbox }, "Box vector lengths (a,b,c)" },
{ "-angles", FALSE, etRVEC,
{ newang }, "Angles between the box vectors (bc,ac,ab)" },
{ "-d", FALSE, etREAL,
{ &dist }, "Distance between the solute and the box" },
{ "-c", FALSE, etBOOL,
{ &bCenter },
"Center molecule in box (implied by -box and -d)" },
{ "-center", FALSE, etRVEC,
{ center }, "Coordinates of geometrical center" },
{ "-aligncenter", FALSE, etRVEC,
{ aligncenter }, "Center of rotation for alignment" },
{ "-align", FALSE, etRVEC,
{ targetvec },
"Align to target vector" },
{ "-translate", FALSE, etRVEC,
{ translation }, "Translation" },
{ "-rotate", FALSE, etRVEC,
{ rotangles },
"Rotation around the X, Y and Z axes in degrees" },
{ "-princ", FALSE, etBOOL,
{ &bOrient },
"Orient molecule(s) along their principal axes" },
{ "-scale", FALSE, etRVEC,
{ scale }, "Scaling factor" },
{ "-density", FALSE, etREAL,
{ &rho },
"Density (g/l) of the output box achieved by scaling" },
{ "-pbc", FALSE, etBOOL,
{ &bRMPBC },
"Remove the periodicity (make molecule whole again)" },
{ "-grasp", FALSE, etBOOL,
{ &bGrasp },
"Store the charge of the atom in the B-factor field and the radius of the atom in the occupancy field" },
{
"-rvdw", FALSE, etREAL,
{ &rvdw },
"Default Van der Waals radius (in nm) if one can not be found in the database or if no parameters are present in the topology file" },
{ "-sig56", FALSE, etREAL,
{ &bSig56 },
"Use rmin/2 (minimum in the Van der Waals potential) rather than sigma/2 " },
{
"-vdwread", FALSE, etBOOL,
{ &bReadVDW },
"Read the Van der Waals radii from the file vdwradii.dat rather than computing the radii based on the force field" },
{ "-atom", FALSE, etBOOL,
{ &peratom }, "Force B-factor attachment per atom" },
{ "-legend", FALSE, etBOOL,
{ &bLegend }, "Make B-factor legend" },
{ "-label", FALSE, etSTR,
{ &label }, "Add chain label for all residues" },
{
"-conect", FALSE, etBOOL,
{ &bCONECT },
"Add CONECT records to a pdb file when written. Can only be done when a topology is present" } };
#define NPA asize(pa)
FILE *out;
const char *infile, *outfile;
char title[STRLEN];
int outftp, inftp, natom, i, j, n_bfac, itype, ntype;
double *bfac = NULL, c6, c12;
int *bfac_nr = NULL;
t_topology *top = NULL;
t_atoms atoms;
char *grpname, *sgrpname, *agrpname;
int isize, ssize, tsize, asize;
atom_id *index, *sindex, *tindex, *aindex;
rvec *x, *v, gc, min, max, size;
int ePBC;
matrix box,rotmatrix,trans;
rvec princd,tmpvec;
gmx_bool bIndex, bSetSize, bSetAng, bCubic, bDist, bSetCenter, bAlign;
gmx_bool bHaveV, bScale, bRho, bTranslate, bRotate, bCalcGeom, bCalcDiam;
real xs, ys, zs, xcent, ycent, zcent, diam = 0, mass = 0, d, vdw;
gmx_atomprop_t aps;
gmx_conect conect;
output_env_t oenv;
t_filenm fnm[] =
{
{ efSTX, "-f", NULL, ffREAD },
{ efNDX, "-n", NULL, ffOPTRD },
{ efSTO, NULL, NULL, ffOPTWR },
{ efPQR, "-mead", "mead", ffOPTWR },
{ efDAT, "-bf", "bfact", ffOPTRD } };
#define NFILE asize(fnm)
CopyRight(stderr, argv[0]);
parse_common_args(&argc, argv, PCA_CAN_VIEW, NFILE, fnm, NPA, pa,
asize(desc), desc, asize(bugs), bugs, &oenv);
bIndex = opt2bSet("-n", NFILE, fnm) || bNDEF;
bMead = opt2bSet("-mead", NFILE, fnm);
bSetSize = opt2parg_bSet("-box", NPA, pa);
bSetAng = opt2parg_bSet("-angles", NPA, pa);
bSetCenter = opt2parg_bSet("-center", NPA, pa);
bDist = opt2parg_bSet("-d", NPA, pa);
bAlign = opt2parg_bSet("-align", NPA, pa);
/* Only automatically turn on centering without -noc */
if ((bDist || bSetSize || bSetCenter) && !opt2parg_bSet("-c", NPA, pa))
{
bCenter = TRUE;
}
bScale = opt2parg_bSet("-scale", NPA, pa);
bRho = opt2parg_bSet("-density", NPA, pa);
bTranslate = opt2parg_bSet("-translate", NPA, pa);
bRotate = opt2parg_bSet("-rotate", NPA, pa);
if (bScale && bRho)
fprintf(stderr, "WARNING: setting -density overrides -scale\n");
bScale = bScale || bRho;
bCalcGeom = bCenter || bRotate || bOrient || bScale;
bCalcDiam = btype[0][0] == 'c' || btype[0][0] == 'd' || btype[0][0] == 'o';
infile = ftp2fn(efSTX, NFILE, fnm);
if (bMead)
outfile = ftp2fn(efPQR, NFILE, fnm);
else
outfile = ftp2fn(efSTO, NFILE, fnm);
outftp = fn2ftp(outfile);
inftp = fn2ftp(infile);
aps = gmx_atomprop_init();
if (bMead && bGrasp)
{
printf("Incompatible options -mead and -grasp. Turning off -grasp\n");
bGrasp = FALSE;
}
if (bGrasp && (outftp != efPDB))
gmx_fatal(FARGS, "Output file should be a .pdb file"
" when using the -grasp option\n");
if ((bMead || bGrasp) && !((fn2ftp(infile) == efTPR) ||
(fn2ftp(infile) == efTPA) ||
(fn2ftp(infile) == efTPB)))
gmx_fatal(FARGS,"Input file should be a .tp[abr] file"
" when using the -mead option\n");
get_stx_coordnum(infile,&natom);
init_t_atoms(&atoms,natom,TRUE);
snew(x,natom);
snew(v,natom);
read_stx_conf(infile,title,&atoms,x,v,&ePBC,box);
if (fn2ftp(infile) == efPDB)
{
get_pdb_atomnumber(&atoms,aps);
}
printf("Read %d atoms\n",atoms.nr);
/* Get the element numbers if available in a pdb file */
if (fn2ftp(infile) == efPDB)
get_pdb_atomnumber(&atoms,aps);
if (ePBC != epbcNONE)
{
real vol = det(box);
printf("Volume: %g nm^3, corresponds to roughly %d electrons\n",
vol,100*((int)(vol*4.5)));
}
if (bMead || bGrasp || bCONECT)
top = read_top(infile,NULL);
if (bMead || bGrasp)
{
if (atoms.nr != top->atoms.nr)
gmx_fatal(FARGS,"Atom numbers don't match (%d vs. %d)",atoms.nr,top->atoms.nr);
snew(atoms.pdbinfo,top->atoms.nr);
ntype = top->idef.atnr;
for(i=0; (i<atoms.nr); i++) {
/* Determine the Van der Waals radius from the force field */
if (bReadVDW) {
if (!gmx_atomprop_query(aps,epropVDW,
*top->atoms.resinfo[top->atoms.atom[i].resind].name,
*top->atoms.atomname[i],&vdw))
vdw = rvdw;
}
else {
itype = top->atoms.atom[i].type;
c12 = top->idef.iparams[itype*ntype+itype].lj.c12;
c6 = top->idef.iparams[itype*ntype+itype].lj.c6;
if ((c6 != 0) && (c12 != 0)) {
real sig6;
if (bSig56)
sig6 = 2*c12/c6;
else
sig6 = c12/c6;
vdw = 0.5*pow(sig6,1.0/6.0);
}
else
vdw = rvdw;
}
/* Factor of 10 for nm -> Angstroms */
vdw *= 10;
if (bMead) {
atoms.pdbinfo[i].occup = top->atoms.atom[i].q;
atoms.pdbinfo[i].bfac = vdw;
}
else {
atoms.pdbinfo[i].occup = vdw;
atoms.pdbinfo[i].bfac = top->atoms.atom[i].q;
}
}
}
bHaveV=FALSE;
for (i=0; (i<natom) && !bHaveV; i++)
for (j=0; (j<DIM) && !bHaveV; j++)
bHaveV=bHaveV || (v[i][j]!=0);
printf("%selocities found\n",bHaveV?"V":"No v");
if (visbox[0] > 0) {
if (bIndex)
gmx_fatal(FARGS,"Sorry, can not visualize box with index groups");
if (outftp != efPDB)
gmx_fatal(FARGS,"Sorry, can only visualize box with a pdb file");
} else if (visbox[0] == -1)
visualize_images("images.pdb",ePBC,box);
/* remove pbc */
if (bRMPBC)
rm_gropbc(&atoms,x,box);
if (bCalcGeom) {
if (bIndex) {
fprintf(stderr,"\nSelect a group for determining the system size:\n");
get_index(&atoms,ftp2fn_null(efNDX,NFILE,fnm),
1,&ssize,&sindex,&sgrpname);
} else {
ssize = atoms.nr;
sindex = NULL;
}
diam=calc_geom(ssize,sindex,x,gc,min,max,bCalcDiam);
rvec_sub(max, min, size);
printf(" system size :%7.3f%7.3f%7.3f (nm)\n",
size[XX], size[YY], size[ZZ]);
if (bCalcDiam)
printf(" diameter :%7.3f (nm)\n",diam);
printf(" center :%7.3f%7.3f%7.3f (nm)\n", gc[XX], gc[YY], gc[ZZ]);
printf(" box vectors :%7.3f%7.3f%7.3f (nm)\n",
norm(box[XX]), norm(box[YY]), norm(box[ZZ]));
printf(" box angles :%7.2f%7.2f%7.2f (degrees)\n",
norm2(box[ZZ])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[YY],box[ZZ])),
norm2(box[ZZ])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[XX],box[ZZ])),
norm2(box[YY])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[XX],box[YY])));
printf(" box volume :%7.2f (nm^3)\n",det(box));
}
if (bRho || bOrient || bAlign)
mass = calc_mass(&atoms,!fn2bTPX(infile),aps);
if (bOrient) {
atom_id *index;
char *grpnames;
/* Get a group for principal component analysis */
fprintf(stderr,"\nSelect group for the determining the orientation\n");
get_index(&atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&isize,&index,&grpnames);
/* Orient the principal axes along the coordinate axes */
orient_princ(&atoms,isize,index,natom,x,bHaveV ? v : NULL, NULL);
sfree(index);
sfree(grpnames);
}
if ( bScale ) {
/* scale coordinates and box */
if (bRho) {
/* Compute scaling constant */
real vol,dens;
vol = det(box);
dens = (mass*AMU)/(vol*NANO*NANO*NANO);
fprintf(stderr,"Volume of input %g (nm^3)\n",vol);
fprintf(stderr,"Mass of input %g (a.m.u.)\n",mass);
fprintf(stderr,"Density of input %g (g/l)\n",dens);
if (vol==0 || mass==0)
gmx_fatal(FARGS,"Cannot scale density with "
"zero mass (%g) or volume (%g)\n",mass,vol);
scale[XX] = scale[YY] = scale[ZZ] = pow(dens/rho,1.0/3.0);
fprintf(stderr,"Scaling all box vectors by %g\n",scale[XX]);
}
scale_conf(atoms.nr,x,box,scale);
}
if (bAlign) {
if (bIndex) {
fprintf(stderr,"\nSelect a group that you want to align:\n");
get_index(&atoms,ftp2fn_null(efNDX,NFILE,fnm),
1,&asize,&aindex,&agrpname);
} else {
asize = atoms.nr;
snew(aindex,asize);
for (i=0;i<asize;i++)
aindex[i]=i;
}
printf("Aligning %d atoms (out of %d) to %g %g %g, center of rotation %g %g %g\n",asize,natom,
targetvec[XX],targetvec[YY],targetvec[ZZ],
aligncenter[XX],aligncenter[YY],aligncenter[ZZ]);
/*subtract out pivot point*/
for(i=0; i<asize; i++)
rvec_dec(x[aindex[i]],aligncenter);
/*now determine transform and rotate*/
/*will this work?*/
principal_comp(asize,aindex,atoms.atom,x, trans,princd);
unitv(targetvec,targetvec);
printf("Using %g %g %g as principal axis\n", trans[0][2],trans[1][2],trans[2][2]);
tmpvec[XX]=trans[0][2]; tmpvec[YY]=trans[1][2]; tmpvec[ZZ]=trans[2][2];
calc_rotmatrix(tmpvec, targetvec, rotmatrix);
/* rotmatrix finished */
for (i=0;i<asize;++i)
{
mvmul(rotmatrix,x[aindex[i]],tmpvec);
copy_rvec(tmpvec,x[aindex[i]]);
}
/*add pivot point back*/
for(i=0; i<asize; i++)
rvec_inc(x[aindex[i]],aligncenter);
if (!bIndex)
sfree(aindex);
}
if (bTranslate) {
if (bIndex) {
fprintf(stderr,"\nSelect a group that you want to translate:\n");
get_index(&atoms,ftp2fn_null(efNDX,NFILE,fnm),
1,&ssize,&sindex,&sgrpname);
} else {
ssize = atoms.nr;
sindex = NULL;
}
printf("Translating %d atoms (out of %d) by %g %g %g nm\n",ssize,natom,
translation[XX],translation[YY],translation[ZZ]);
if (sindex) {
for(i=0; i<ssize; i++)
rvec_inc(x[sindex[i]],translation);
}
else {
for(i=0; i<natom; i++)
rvec_inc(x[i],translation);
}
}
if (bRotate) {
/* Rotate */
printf("Rotating %g, %g, %g degrees around the X, Y and Z axis respectively\n",rotangles[XX],rotangles[YY],rotangles[ZZ]);
for(i=0; i<DIM; i++)
rotangles[i] *= DEG2RAD;
rotate_conf(natom,x,v,rotangles[XX],rotangles[YY],rotangles[ZZ]);
}
if (bCalcGeom) {
/* recalc geometrical center and max and min coordinates and size */
calc_geom(ssize,sindex,x,gc,min,max,FALSE);
rvec_sub(max, min, size);
if (bScale || bOrient || bRotate)
printf("new system size : %6.3f %6.3f %6.3f\n",
size[XX],size[YY],size[ZZ]);
}
if (bSetSize || bDist || (btype[0][0]=='t' && bSetAng)) {
ePBC = epbcXYZ;
if (!(bSetSize || bDist))
for (i=0; i<DIM; i++)
newbox[i] = norm(box[i]);
clear_mat(box);
/* calculate new boxsize */
switch(btype[0][0]){
case 't':
if (bDist)
for(i=0; i<DIM; i++)
newbox[i] = size[i]+2*dist;
if (!bSetAng) {
box[XX][XX] = newbox[XX];
box[YY][YY] = newbox[YY];
box[ZZ][ZZ] = newbox[ZZ];
} else {
matrix_convert(box,newbox,newang);
}
break;
case 'c':
case 'd':
case 'o':
if (bSetSize)
d = newbox[0];
else
d = diam+2*dist;
if (btype[0][0] == 'c')
for(i=0; i<DIM; i++)
box[i][i] = d;
else if (btype[0][0] == 'd') {
box[XX][XX] = d;
box[YY][YY] = d;
box[ZZ][XX] = d/2;
box[ZZ][YY] = d/2;
box[ZZ][ZZ] = d*sqrt(2)/2;
} else {
box[XX][XX] = d;
box[YY][XX] = d/3;
box[YY][YY] = d*sqrt(2)*2/3;
box[ZZ][XX] = -d/3;
box[ZZ][YY] = d*sqrt(2)/3;
box[ZZ][ZZ] = d*sqrt(6)/3;
}
break;
}
}
/* calculate new coords for geometrical center */
if (!bSetCenter)
calc_box_center(ecenterDEF,box,center);
/* center molecule on 'center' */
if (bCenter)
center_conf(natom,x,center,gc);
/* print some */
if (bCalcGeom) {
calc_geom(ssize,sindex,x, gc, min, max, FALSE);
printf("new center :%7.3f%7.3f%7.3f (nm)\n",gc[XX],gc[YY],gc[ZZ]);
}
if (bOrient || bScale || bDist || bSetSize) {
printf("new box vectors :%7.3f%7.3f%7.3f (nm)\n",
norm(box[XX]), norm(box[YY]), norm(box[ZZ]));
printf("new box angles :%7.2f%7.2f%7.2f (degrees)\n",
norm2(box[ZZ])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[YY],box[ZZ])),
norm2(box[ZZ])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[XX],box[ZZ])),
norm2(box[YY])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[XX],box[YY])));
printf("new box volume :%7.2f (nm^3)\n",det(box));
}
if (check_box(epbcXYZ,box))
printf("\nWARNING: %s\n",check_box(epbcXYZ,box));
if (bDist && btype[0][0]=='t')
{
if(TRICLINIC(box))
{
printf("\nWARNING: Your box is triclinic with non-orthogonal axes. In this case, the\n"
"distance from the solute to a box surface along the corresponding normal\n"
"vector might be somewhat smaller than your specified value %f.\n"
"You can check the actual value with g_mindist -pi\n",dist);
}
else
{
printf("\nWARNING: No boxtype specified - distance condition applied in each dimension.\n"
"If the molecule rotates the actual distance will be smaller. You might want\n"
"to use a cubic box instead, or why not try a dodecahedron today?\n");
}
}
if (bCONECT && (outftp == efPDB) && (inftp == efTPR))
conect = gmx_conect_generate(top);
else
conect = NULL;
if (bIndex) {
fprintf(stderr,"\nSelect a group for output:\n");
get_index(&atoms,opt2fn_null("-n",NFILE,fnm),
1,&isize,&index,&grpname);
if (opt2parg_bSet("-label",NPA,pa)) {
for(i=0; (i<atoms.nr); i++)
atoms.resinfo[atoms.atom[i].resind].chainid=label[0];
}
if (opt2bSet("-bf",NFILE,fnm) || bLegend)
{
gmx_fatal(FARGS,"Sorry, cannot do bfactors with an index group.");
}
if (outftp == efPDB)
{
out=ffopen(outfile,"w");
write_pdbfile_indexed(out,title,&atoms,x,ePBC,box,' ',1,isize,index,conect,TRUE);
ffclose(out);
}
else
{
write_sto_conf_indexed(outfile,title,&atoms,x,bHaveV?v:NULL,ePBC,box,isize,index);
}
}
else {
if ((outftp == efPDB) || (outftp == efPQR)) {
out=ffopen(outfile,"w");
if (bMead) {
set_pdb_wide_format(TRUE);
fprintf(out,"REMARK "
"The B-factors in this file hold atomic radii\n");
fprintf(out,"REMARK "
"The occupancy in this file hold atomic charges\n");
}
else if (bGrasp) {
fprintf(out,"GRASP PDB FILE\nFORMAT NUMBER=1\n");
fprintf(out,"REMARK "
"The B-factors in this file hold atomic charges\n");
fprintf(out,"REMARK "
"The occupancy in this file hold atomic radii\n");
}
else if (opt2bSet("-bf",NFILE,fnm)) {
read_bfac(opt2fn("-bf",NFILE,fnm),&n_bfac,&bfac,&bfac_nr);
set_pdb_conf_bfac(atoms.nr,atoms.nres,&atoms,
n_bfac,bfac,bfac_nr,peratom);
}
if (opt2parg_bSet("-label",NPA,pa)) {
for(i=0; (i<atoms.nr); i++)
atoms.resinfo[atoms.atom[i].resind].chainid=label[0];
}
write_pdbfile(out,title,&atoms,x,ePBC,box,' ',-1,conect,TRUE);
if (bLegend)
pdb_legend(out,atoms.nr,atoms.nres,&atoms,x);
if (visbox[0] > 0)
visualize_box(out,bLegend ? atoms.nr+12 : atoms.nr,
bLegend? atoms.nres=12 : atoms.nres,box,visbox);
ffclose(out);
}
else
write_sto_conf(outfile,title,&atoms,x,bHaveV?v:NULL,ePBC,box);
}
gmx_atomprop_destroy(aps);
do_view(oenv,outfile,NULL);
thanx(stderr);
return 0;
}
real
do_listed_vdw_q(int ftype,int nbonds,
const t_iatom iatoms[],const t_iparams iparams[],
const rvec x[],rvec f[],rvec fshift[],
const t_pbc *pbc,const t_graph *g,
real lambda,real *dvdlambda,
const t_mdatoms *md,
const t_forcerec *fr,gmx_grppairener_t *grppener,
int *global_atom_index)
{
static gmx_bool bWarn=FALSE;
real eps,r2,*tab,rtab2=0;
rvec dx,x14[2],f14[2];
int i,ai,aj,itype;
int typeA[2]={0,0},typeB[2]={0,1};
real chargeA[2]={0,0},chargeB[2];
int gid,shift_vir,shift_f;
int j_index[] = { 0, 1 };
int i0=0,i1=1,i2=2;
ivec dt;
int outeriter,inneriter;
int nthreads = 1;
int count;
real krf,crf,tabscale;
int ntype=0;
real *nbfp=NULL;
real *egnb=NULL,*egcoul=NULL;
t_nblist tmplist;
int icoul,ivdw;
gmx_bool bMolPBC,bFreeEnergy;
t_pf_global *pf_global;
#if GMX_THREAD_SHM_FDECOMP
pthread_mutex_t mtx;
#else
void * mtx = NULL;
#endif
#if GMX_THREAD_SHM_FDECOMP
pthread_mutex_initialize(&mtx);
#endif
bMolPBC = fr->bMolPBC;
pf_global = fr->pf_global;
switch (ftype) {
case F_LJ14:
case F_LJC14_Q:
eps = fr->epsfac*fr->fudgeQQ;
ntype = 1;
egnb = grppener->ener[egLJ14];
egcoul = grppener->ener[egCOUL14];
break;
case F_LJC_PAIRS_NB:
eps = fr->epsfac;
ntype = 1;
egnb = grppener->ener[egLJSR];
egcoul = grppener->ener[egCOULSR];
break;
default:
gmx_fatal(FARGS,"Unknown function type %d in do_nonbonded14",
ftype);
}
tab = fr->tab14.tab;
rtab2 = sqr(fr->tab14.r);
tabscale = fr->tab14.scale;
krf = fr->k_rf;
crf = fr->c_rf;
/* Determine the values for icoul/ivdw. */
if (fr->bEwald) {
icoul = 1;
}
else if(fr->bcoultab)
{
icoul = 3;
}
else if(fr->eeltype == eelRF_NEC)
{
icoul = 2;
}
else
{
icoul = 1;
}
if(fr->bvdwtab)
{
ivdw = 3;
}
else if(fr->bBHAM)
{
ivdw = 2;
}
else
{
ivdw = 1;
}
/* We don't do SSE or altivec here, due to large overhead for 4-fold
* unrolling on short lists
*/
bFreeEnergy = FALSE;
for(i=0; (i<nbonds); )
{
itype = iatoms[i++];
ai = iatoms[i++];
aj = iatoms[i++];
gid = GID(md->cENER[ai],md->cENER[aj],md->nenergrp);
switch (ftype) {
case F_LJ14:
bFreeEnergy =
(fr->efep != efepNO &&
((md->nPerturbed && (md->bPerturbed[ai] || md->bPerturbed[aj])) ||
iparams[itype].lj14.c6A != iparams[itype].lj14.c6B ||
iparams[itype].lj14.c12A != iparams[itype].lj14.c12B));
chargeA[0] = md->chargeA[ai];
chargeA[1] = md->chargeA[aj];
nbfp = (real *)&(iparams[itype].lj14.c6A);
break;
case F_LJC14_Q:
eps = fr->epsfac*iparams[itype].ljc14.fqq;
chargeA[0] = iparams[itype].ljc14.qi;
chargeA[1] = iparams[itype].ljc14.qj;
nbfp = (real *)&(iparams[itype].ljc14.c6);
break;
case F_LJC_PAIRS_NB:
chargeA[0] = iparams[itype].ljcnb.qi;
chargeA[1] = iparams[itype].ljcnb.qj;
nbfp = (real *)&(iparams[itype].ljcnb.c6);
break;
}
if (!bMolPBC)
{
/* This is a bonded interaction, atoms are in the same box */
shift_f = CENTRAL;
r2 = distance2(x[ai],x[aj]);
}
else
{
/* Apply full periodic boundary conditions */
shift_f = pbc_dx_aiuc(pbc,x[ai],x[aj],dx);
r2 = norm2(dx);
}
if (r2 >= rtab2)
{
if (!bWarn)
{
fprintf(stderr,"Warning: 1-4 interaction between %d and %d "
"at distance %.3f which is larger than the 1-4 table size %.3f nm\n",
glatnr(global_atom_index,ai),
glatnr(global_atom_index,aj),
sqrt(r2), sqrt(rtab2));
fprintf(stderr,"These are ignored for the rest of the simulation\n");
fprintf(stderr,"This usually means your system is exploding,\n"
"if not, you should increase table-extension in your mdp file\n"
"or with user tables increase the table size\n");
bWarn = TRUE;
}
if (debug)
fprintf(debug,"%8f %8f %8f\n%8f %8f %8f\n1-4 (%d,%d) interaction not within cut-off! r=%g. Ignored\n",
x[ai][XX],x[ai][YY],x[ai][ZZ],
x[aj][XX],x[aj][YY],x[aj][ZZ],
glatnr(global_atom_index,ai),
glatnr(global_atom_index,aj),
sqrt(r2));
}
else
{
copy_rvec(x[ai],x14[0]);
copy_rvec(x[aj],x14[1]);
clear_rvec(f14[0]);
clear_rvec(f14[1]);
#ifdef DEBUG
fprintf(debug,"LJ14: grp-i=%2d, grp-j=%2d, ngrp=%2d, GID=%d\n",
md->cENER[ai],md->cENER[aj],md->nenergrp,gid);
#endif
outeriter = inneriter = count = 0;
if (bFreeEnergy)
{
chargeB[0] = md->chargeB[ai];
chargeB[1] = md->chargeB[aj];
/* We pass &(iparams[itype].lj14.c6A) as LJ parameter matrix
* to the innerloops.
* Here we use that the LJ-14 parameters are stored in iparams
* as c6A,c12A,c6B,c12B, which are referenced correctly
* in the innerloops if we assign type combinations 0-0 and 0-1
* to atom pair ai-aj in topologies A and B respectively.
*/
if(ivdw==2)
{
gmx_fatal(FARGS,"Cannot do free energy Buckingham interactions.");
}
count = 0;
gmx_nb_free_energy_kernel(icoul,
ivdw,
i1,
&i0,
j_index,
&i1,
&shift_f,
fr->shift_vec[0],
fshift[0],
&gid,
x14[0],
f14[0],
chargeA,
chargeB,
eps,
krf,
crf,
fr->ewaldcoeff,
egcoul,
typeA,
typeB,
ntype,
nbfp,
egnb,
tabscale,
tab,
lambda,
dvdlambda,
fr->sc_alpha,
fr->sc_power,
fr->sc_sigma6_def,
fr->sc_sigma6_min,
TRUE,
&outeriter,
&inneriter);
}
else
{
/* Not perturbed - call kernel 330 */
nb_kernel330
( &i1,
&i0,
j_index,
&i1,
&shift_f,
fr->shift_vec[0],
fshift[0],
&gid,
x14[0],
f14[0],
chargeA,
&eps,
&krf,
&crf,
egcoul,
typeA,
&ntype,
nbfp,
egnb,
&tabscale,
tab,
NULL,
NULL,
NULL,
NULL,
&nthreads,
&count,
(void *)&mtx,
&outeriter,
&inneriter,
NULL);
}
/* Add the forces */
rvec_inc(f[ai],f14[0]);
rvec_dec(f[aj],f14[0]);
if (pf_global->bInitialized)
pf_atom_add_bonded(pf_global, ai, aj, PF_INTER_NB14, f14[0]);
if (g)
{
/* Correct the shift forces using the graph */
ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,aj),dt);
shift_vir = IVEC2IS(dt);
rvec_inc(fshift[shift_vir],f14[0]);
rvec_dec(fshift[CENTRAL],f14[0]);
}
/* flops: eNR_KERNEL_OUTER + eNR_KERNEL330 + 12 */
}
}
return 0.0;
}
void add_conf(t_atoms *atoms, rvec **x, rvec **v, real **r, gmx_bool bSrenew,
int ePBC, matrix box, gmx_bool bInsert,
t_atoms *atoms_solvt, rvec *x_solvt, rvec *v_solvt, real *r_solvt,
gmx_bool bVerbose, real rshell, int max_sol, const output_env_t oenv)
{
t_nblist *nlist;
t_atoms *atoms_all;
real max_vdw, *r_prot, *r_all, n2, r2, ib1, ib2;
int natoms_prot, natoms_solvt;
int i, j, jj, m, j0, j1, jjj, jnres, jnr, inr, iprot, is1, is2;
int prev, resnr, nresadd, d, k, ncells, maxincell;
int dx0, dx1, dy0, dy1, dz0, dz1;
int ntest, nremove, nkeep;
rvec dx, xi, xj, xpp, *x_all, *v_all;
gmx_bool *remove, *keep;
int bSolSol;
natoms_prot = atoms->nr;
natoms_solvt = atoms_solvt->nr;
if (natoms_solvt <= 0)
{
fprintf(stderr, "WARNING: Nothing to add\n");
return;
}
if (ePBC == epbcSCREW)
{
gmx_fatal(FARGS, "Sorry, %s pbc is not yet supported", epbc_names[ePBC]);
}
if (bVerbose)
{
fprintf(stderr, "Calculating Overlap...\n");
}
/* Set margin around box edges to largest solvent dimension.
* The maximum distance between atoms in a solvent molecule should
* be calculated. At the moment a fudge factor of 3 is used.
*/
r_prot = *r;
box_margin = 3*find_max_real(natoms_solvt, r_solvt);
max_vdw = max(3*find_max_real(natoms_prot, r_prot), box_margin);
fprintf(stderr, "box_margin = %g\n", box_margin);
snew(remove, natoms_solvt);
nremove = 0;
if (!bInsert)
{
for (i = 0; i < atoms_solvt->nr; i++)
{
if (outside_box_plus_margin(x_solvt[i], box) )
{
i = mark_res(i, remove, atoms_solvt->nr, atoms_solvt->atom, &nremove);
}
}
fprintf(stderr, "Removed %d atoms that were outside the box\n", nremove);
}
/* Define grid stuff for genbox */
/* Largest VDW radius */
snew(r_all, natoms_prot+natoms_solvt);
for (i = j = 0; i < natoms_prot; i++, j++)
{
r_all[j] = r_prot[i];
}
for (i = 0; i < natoms_solvt; i++, j++)
{
r_all[j] = r_solvt[i];
}
/* Combine arrays */
combine_atoms(atoms, atoms_solvt, *x, v ? *v : NULL, x_solvt, v_solvt,
&atoms_all, &x_all, &v_all);
/* Do neighboursearching step */
do_nsgrid(stdout, bVerbose, box, x_all, atoms_all, max_vdw, oenv);
/* check solvent with solute */
nlist = &(fr->nblists[0].nlist_sr[eNL_VDW]);
fprintf(stderr, "nri = %d, nrj = %d\n", nlist->nri, nlist->nrj);
for (bSolSol = 0; (bSolSol <= (bInsert ? 0 : 1)); bSolSol++)
{
ntest = nremove = 0;
fprintf(stderr, "Checking %s-Solvent overlap:",
bSolSol ? "Solvent" : "Protein");
for (i = 0; (i < nlist->nri && nremove < natoms_solvt); i++)
{
inr = nlist->iinr[i];
j0 = nlist->jindex[i];
j1 = nlist->jindex[i+1];
rvec_add(x_all[inr], fr->shift_vec[nlist->shift[i]], xi);
for (j = j0; (j < j1 && nremove < natoms_solvt); j++)
{
jnr = nlist->jjnr[j];
copy_rvec(x_all[jnr], xj);
/* Check solvent-protein and solvent-solvent */
is1 = inr-natoms_prot;
is2 = jnr-natoms_prot;
/* Check if at least one of the atoms is a solvent that is not yet
* listed for removal, and if both are solvent, that they are not in the
* same residue.
*/
if ((!bSolSol &&
bXor((is1 >= 0), (is2 >= 0)) && /* One atom is protein */
((is1 < 0) || ((is1 >= 0) && !remove[is1])) &&
((is2 < 0) || ((is2 >= 0) && !remove[is2]))) ||
(bSolSol &&
(is1 >= 0) && (!remove[is1]) && /* is1 is solvent */
(is2 >= 0) && (!remove[is2]) && /* is2 is solvent */
(bInsert || /* when inserting also check inside the box */
(outside_box_minus_margin2(x_solvt[is1], box) && /* is1 on edge */
outside_box_minus_margin2(x_solvt[is2], box)) /* is2 on edge */
) &&
(atoms_solvt->atom[is1].resind != /* Not the same residue */
atoms_solvt->atom[is2].resind)))
{
ntest++;
rvec_sub(xi, xj, dx);
n2 = norm2(dx);
r2 = sqr(r_all[inr]+r_all[jnr]);
if (n2 < r2)
{
if (bInsert)
{
nremove = natoms_solvt;
for (k = 0; k < nremove; k++)
{
remove[k] = TRUE;
}
}
/* Need only remove one of the solvents... */
if (is2 >= 0)
{
(void) mark_res(is2, remove, natoms_solvt, atoms_solvt->atom,
&nremove);
}
else if (is1 >= 0)
{
(void) mark_res(is1, remove, natoms_solvt, atoms_solvt->atom,
&nremove);
}
else
{
fprintf(stderr, "Neither atom is solvent%d %d\n", is1, is2);
}
}
}
}
}
if (!bInsert)
{
fprintf(stderr, " tested %d pairs, removed %d atoms.\n", ntest, nremove);
}
}
if (debug)
{
for (i = 0; i < natoms_solvt; i++)
{
fprintf(debug, "remove[%5d] = %s\n", i, bool_names[remove[i]]);
}
}
/* Search again, now with another cut-off */
if (rshell > 0)
{
do_nsgrid(stdout, bVerbose, box, x_all, atoms_all, rshell, oenv);
nlist = &(fr->nblists[0].nlist_sr[eNL_VDW]);
fprintf(stderr, "nri = %d, nrj = %d\n", nlist->nri, nlist->nrj);
nkeep = 0;
snew(keep, natoms_solvt);
for (i = 0; i < nlist->nri; i++)
{
inr = nlist->iinr[i];
j0 = nlist->jindex[i];
j1 = nlist->jindex[i+1];
for (j = j0; j < j1; j++)
{
jnr = nlist->jjnr[j];
/* Check solvent-protein and solvent-solvent */
is1 = inr-natoms_prot;
is2 = jnr-natoms_prot;
/* Check if at least one of the atoms is a solvent that is not yet
* listed for removal, and if both are solvent, that they are not in the
* same residue.
*/
if (is1 >= 0 && is2 < 0)
{
mark_res(is1, keep, natoms_solvt, atoms_solvt->atom, &nkeep);
}
else if (is1 < 0 && is2 >= 0)
{
mark_res(is2, keep, natoms_solvt, atoms_solvt->atom, &nkeep);
}
}
}
fprintf(stderr, "Keeping %d solvent atoms after proximity check\n",
nkeep);
for (i = 0; i < natoms_solvt; i++)
{
remove[i] = remove[i] || !keep[i];
}
sfree(keep);
}
/* count how many atoms and residues will be added and make space */
if (bInsert)
{
j = atoms_solvt->nr;
jnres = atoms_solvt->nres;
}
else
{
j = 0;
jnres = 0;
for (i = 0; ((i < atoms_solvt->nr) &&
((max_sol == 0) || (jnres < max_sol))); i++)
{
if (!remove[i])
{
j++;
if ((i == 0) ||
(atoms_solvt->atom[i].resind != atoms_solvt->atom[i-1].resind))
{
jnres++;
}
}
}
}
if (debug)
{
fprintf(debug, "Will add %d atoms in %d residues\n", j, jnres);
}
if (!bInsert)
{
/* Flag the remaing solvent atoms to be removed */
jjj = atoms_solvt->atom[i-1].resind;
for (; (i < atoms_solvt->nr); i++)
{
if (atoms_solvt->atom[i].resind > jjj)
{
remove[i] = TRUE;
}
else
{
j++;
}
}
}
if (bSrenew)
{
srenew(atoms->resinfo, atoms->nres+jnres);
srenew(atoms->atomname, atoms->nr+j);
srenew(atoms->atom, atoms->nr+j);
srenew(*x, atoms->nr+j);
if (v)
{
srenew(*v, atoms->nr+j);
}
srenew(*r, atoms->nr+j);
}
/* add the selected atoms_solvt to atoms */
if (atoms->nr > 0)
{
resnr = atoms->resinfo[atoms->atom[atoms->nr-1].resind].nr;
}
else
{
resnr = 0;
}
prev = -1;
nresadd = 0;
for (i = 0; i < atoms_solvt->nr; i++)
{
if (!remove[i])
{
if (prev == -1 ||
atoms_solvt->atom[i].resind != atoms_solvt->atom[prev].resind)
{
nresadd++;
atoms->nres++;
resnr++;
atoms->resinfo[atoms->nres-1] =
atoms_solvt->resinfo[atoms_solvt->atom[i].resind];
atoms->resinfo[atoms->nres-1].nr = resnr;
/* calculate shift of the solvent molecule using the first atom */
copy_rvec(x_solvt[i], dx);
put_atoms_in_box(ePBC, box, 1, &dx);
rvec_dec(dx, x_solvt[i]);
}
atoms->atom[atoms->nr] = atoms_solvt->atom[i];
atoms->atomname[atoms->nr] = atoms_solvt->atomname[i];
rvec_add(x_solvt[i], dx, (*x)[atoms->nr]);
if (v)
{
copy_rvec(v_solvt[i], (*v)[atoms->nr]);
}
(*r)[atoms->nr] = r_solvt[i];
atoms->atom[atoms->nr].resind = atoms->nres-1;
atoms->nr++;
prev = i;
}
}
if (bSrenew)
{
srenew(atoms->resinfo, atoms->nres+nresadd);
}
if (bVerbose)
{
fprintf(stderr, "Added %d molecules\n", nresadd);
}
sfree(remove);
done_atom(atoms_all);
sfree(x_all);
sfree(v_all);
}
real ewald_LRcorrection(FILE *fplog,
int start, int end,
t_commrec *cr, int thread, t_forcerec *fr,
real *chargeA, real *chargeB,
gmx_bool calc_excl_corr,
t_blocka *excl, rvec x[],
matrix box, rvec mu_tot[],
int ewald_geometry, real epsilon_surface,
rvec *f, tensor vir,
real lambda, real *dvdlambda)
{
int i, i1, i2, j, k, m, iv, jv, q;
atom_id *AA;
double q2sumA, q2sumB, Vexcl, dvdl_excl; /* Necessary for precision */
real one_4pi_eps;
real v, vc, qiA, qiB, dr, dr2, rinv, fscal, enercorr;
real Vself[2], Vdipole[2], rinv2, ewc = fr->ewaldcoeff, ewcdr;
rvec df, dx, mutot[2], dipcorrA, dipcorrB;
tensor dxdf;
real vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
real L1, dipole_coeff, qqA, qqB, qqL, vr0;
/*#define TABLES*/
#ifdef TABLES
real tabscale = fr->tabscale;
real eps, eps2, VV, FF, F, Y, Geps, Heps2, Fp, fijC, r1t;
real *VFtab = fr->coulvdwtab;
int n0, n1, nnn;
#endif
gmx_bool bFreeEnergy = (chargeB != NULL);
gmx_bool bMolPBC = fr->bMolPBC;
one_4pi_eps = ONE_4PI_EPS0/fr->epsilon_r;
vr0 = ewc*M_2_SQRTPI;
AA = excl->a;
Vexcl = 0;
dvdl_excl = 0;
q2sumA = 0;
q2sumB = 0;
Vdipole[0] = 0;
Vdipole[1] = 0;
L1 = 1.0-lambda;
/* Note that we have to transform back to gromacs units, since
* mu_tot contains the dipole in debye units (for output).
*/
for (i = 0; (i < DIM); i++)
{
mutot[0][i] = mu_tot[0][i]*DEBYE2ENM;
mutot[1][i] = mu_tot[1][i]*DEBYE2ENM;
dipcorrA[i] = 0;
dipcorrB[i] = 0;
}
dipole_coeff = 0;
switch (ewald_geometry)
{
case eewg3D:
if (epsilon_surface != 0)
{
dipole_coeff =
2*M_PI*ONE_4PI_EPS0/((2*epsilon_surface + fr->epsilon_r)*vol);
for (i = 0; (i < DIM); i++)
{
dipcorrA[i] = 2*dipole_coeff*mutot[0][i];
dipcorrB[i] = 2*dipole_coeff*mutot[1][i];
}
}
break;
case eewg3DC:
dipole_coeff = 2*M_PI*one_4pi_eps/vol;
dipcorrA[ZZ] = 2*dipole_coeff*mutot[0][ZZ];
dipcorrB[ZZ] = 2*dipole_coeff*mutot[1][ZZ];
break;
default:
gmx_incons("Unsupported Ewald geometry");
break;
}
if (debug)
{
fprintf(debug, "dipcorr = %8.3f %8.3f %8.3f\n",
dipcorrA[XX], dipcorrA[YY], dipcorrA[ZZ]);
fprintf(debug, "mutot = %8.3f %8.3f %8.3f\n",
mutot[0][XX], mutot[0][YY], mutot[0][ZZ]);
}
clear_mat(dxdf);
if ((calc_excl_corr || dipole_coeff != 0) && !bFreeEnergy)
{
for (i = start; (i < end); i++)
{
/* Initiate local variables (for this i-particle) to 0 */
qiA = chargeA[i]*one_4pi_eps;
if (calc_excl_corr)
{
i1 = excl->index[i];
i2 = excl->index[i+1];
/* Loop over excluded neighbours */
for (j = i1; (j < i2); j++)
{
k = AA[j];
/*
* First we must test whether k <> i, and then, because the
* exclusions are all listed twice i->k and k->i we must select
* just one of the two.
* As a minor optimization we only compute forces when the charges
* are non-zero.
*/
if (k > i)
{
qqA = qiA*chargeA[k];
if (qqA != 0.0)
{
rvec_sub(x[i], x[k], dx);
if (bMolPBC)
{
/* Cheap pbc_dx, assume excluded pairs are at short distance. */
for (m = DIM-1; (m >= 0); m--)
{
if (dx[m] > 0.5*box[m][m])
{
rvec_dec(dx, box[m]);
}
else if (dx[m] < -0.5*box[m][m])
{
rvec_inc(dx, box[m]);
}
}
}
dr2 = norm2(dx);
/* Distance between two excluded particles may be zero in the
* case of shells
*/
if (dr2 != 0)
{
rinv = gmx_invsqrt(dr2);
rinv2 = rinv*rinv;
dr = 1.0/rinv;
#ifdef TABLES
r1t = tabscale*dr;
n0 = r1t;
assert(n0 >= 3);
n1 = 12*n0;
eps = r1t-n0;
eps2 = eps*eps;
nnn = n1;
Y = VFtab[nnn];
F = VFtab[nnn+1];
Geps = eps*VFtab[nnn+2];
Heps2 = eps2*VFtab[nnn+3];
Fp = F+Geps+Heps2;
VV = Y+eps*Fp;
FF = Fp+Geps+2.0*Heps2;
vc = qqA*(rinv-VV);
fijC = qqA*FF;
Vexcl += vc;
fscal = vc*rinv2+fijC*tabscale*rinv;
/* End of tabulated interaction part */
#else
/* This is the code you would want instead if not using
* tables:
*/
ewcdr = ewc*dr;
vc = qqA*gmx_erf(ewcdr)*rinv;
Vexcl += vc;
#ifdef GMX_DOUBLE
/* Relative accuracy at R_ERF_R_INACC of 3e-10 */
#define R_ERF_R_INACC 0.006
#else
/* Relative accuracy at R_ERF_R_INACC of 2e-5 */
#define R_ERF_R_INACC 0.1
#endif
if (ewcdr > R_ERF_R_INACC)
{
fscal = rinv2*(vc - qqA*ewc*M_2_SQRTPI*exp(-ewcdr*ewcdr));
}
else
{
/* Use a fourth order series expansion for small ewcdr */
fscal = ewc*ewc*qqA*vr0*(2.0/3.0 - 0.4*ewcdr*ewcdr);
}
#endif
/* The force vector is obtained by multiplication with the
* distance vector
*/
svmul(fscal, dx, df);
rvec_inc(f[k], df);
rvec_dec(f[i], df);
for (iv = 0; (iv < DIM); iv++)
{
for (jv = 0; (jv < DIM); jv++)
{
dxdf[iv][jv] += dx[iv]*df[jv];
}
}
}
else
{
Vexcl += qqA*vr0;
}
}
}
}
}
/* Dipole correction on force */
if (dipole_coeff != 0)
{
for (j = 0; (j < DIM); j++)
{
f[i][j] -= dipcorrA[j]*chargeA[i];
}
}
}
}
else if (calc_excl_corr || dipole_coeff != 0)
{
for (i = start; (i < end); i++)
{
/* Initiate local variables (for this i-particle) to 0 */
qiA = chargeA[i]*one_4pi_eps;
qiB = chargeB[i]*one_4pi_eps;
if (calc_excl_corr)
{
i1 = excl->index[i];
i2 = excl->index[i+1];
/* Loop over excluded neighbours */
for (j = i1; (j < i2); j++)
{
k = AA[j];
if (k > i)
{
qqA = qiA*chargeA[k];
qqB = qiB*chargeB[k];
if (qqA != 0.0 || qqB != 0.0)
{
qqL = L1*qqA + lambda*qqB;
rvec_sub(x[i], x[k], dx);
if (bMolPBC)
{
/* Cheap pbc_dx, assume excluded pairs are at short distance. */
for (m = DIM-1; (m >= 0); m--)
{
if (dx[m] > 0.5*box[m][m])
{
rvec_dec(dx, box[m]);
}
else if (dx[m] < -0.5*box[m][m])
{
rvec_inc(dx, box[m]);
}
}
}
dr2 = norm2(dx);
if (dr2 != 0)
{
rinv = gmx_invsqrt(dr2);
rinv2 = rinv*rinv;
dr = 1.0/rinv;
v = gmx_erf(ewc*dr)*rinv;
vc = qqL*v;
Vexcl += vc;
fscal = rinv2*(vc-qqL*ewc*M_2_SQRTPI*exp(-ewc*ewc*dr2));
svmul(fscal, dx, df);
rvec_inc(f[k], df);
rvec_dec(f[i], df);
for (iv = 0; (iv < DIM); iv++)
{
for (jv = 0; (jv < DIM); jv++)
{
dxdf[iv][jv] += dx[iv]*df[jv];
}
}
dvdl_excl += (qqB - qqA)*v;
}
else
{
Vexcl += qqL*vr0;
dvdl_excl += (qqB - qqA)*vr0;
}
}
}
}
}
/* Dipole correction on force */
if (dipole_coeff != 0)
{
for (j = 0; (j < DIM); j++)
{
f[i][j] -= L1*dipcorrA[j]*chargeA[i]
+ lambda*dipcorrB[j]*chargeB[i];
}
}
}
}
for (iv = 0; (iv < DIM); iv++)
{
for (jv = 0; (jv < DIM); jv++)
{
vir[iv][jv] += 0.5*dxdf[iv][jv];
}
}
Vself[0] = 0;
Vself[1] = 0;
/* Global corrections only on master process */
if (MASTER(cr) && thread == 0)
{
for (q = 0; q < (bFreeEnergy ? 2 : 1); q++)
{
if (calc_excl_corr)
{
/* Self-energy correction */
Vself[q] = ewc*one_4pi_eps*fr->q2sum[q]*M_1_SQRTPI;
}
/* Apply surface dipole correction:
* correction = dipole_coeff * (dipole)^2
*/
if (dipole_coeff != 0)
{
if (ewald_geometry == eewg3D)
{
Vdipole[q] = dipole_coeff*iprod(mutot[q], mutot[q]);
}
else if (ewald_geometry == eewg3DC)
{
Vdipole[q] = dipole_coeff*mutot[q][ZZ]*mutot[q][ZZ];
}
}
}
}
if (!bFreeEnergy)
{
enercorr = Vdipole[0] - Vself[0] - Vexcl;
}
else
{
enercorr = L1*(Vdipole[0] - Vself[0])
+ lambda*(Vdipole[1] - Vself[1])
- Vexcl;
*dvdlambda += Vdipole[1] - Vself[1]
- (Vdipole[0] - Vself[0]) - dvdl_excl;
}
if (debug)
{
fprintf(debug, "Long Range corrections for Ewald interactions:\n");
fprintf(debug, "start=%d,natoms=%d\n", start, end-start);
fprintf(debug, "q2sum = %g, Vself=%g\n",
L1*q2sumA+lambda*q2sumB, L1*Vself[0]+lambda*Vself[1]);
fprintf(debug, "Long Range correction: Vexcl=%g\n", Vexcl);
if (MASTER(cr) && thread == 0)
{
if (epsilon_surface > 0 || ewald_geometry == eewg3DC)
{
fprintf(debug, "Total dipole correction: Vdipole=%g\n",
L1*Vdipole[0]+lambda*Vdipole[1]);
}
}
}
/* Return the correction to the energy */
return enercorr;
}
real RF_excl_correction(FILE *log,
const t_forcerec *fr,t_graph *g,
const t_mdatoms *mdatoms,const t_blocka *excl,
rvec x[],rvec f[],rvec *fshift,const t_pbc *pbc,
real lambda,real *dvdlambda)
{
/* Calculate the reaction-field energy correction for this node:
* epsfac q_i q_j (k_rf r_ij^2 - c_rf)
* and force correction for all excluded pairs, including self pairs.
*/
int top,i,j,j1,j2,k,ki;
double q2sumA,q2sumB,ener;
const real *chargeA,*chargeB;
real ek,ec,L1,qiA,qiB,qqA,qqB,qqL,v;
rvec dx,df;
atom_id *AA;
ivec dt;
int start = mdatoms->start;
int end = mdatoms->homenr+start;
int niat;
gmx_bool bMolPBC = fr->bMolPBC;
if (fr->n_tpi)
/* For test particle insertion we only correct for the test molecule */
start = mdatoms->nr - fr->n_tpi;
ek = fr->epsfac*fr->k_rf;
ec = fr->epsfac*fr->c_rf;
chargeA = mdatoms->chargeA;
chargeB = mdatoms->chargeB;
AA = excl->a;
ki = CENTRAL;
if (fr->bDomDec)
niat = excl->nr;
else
niat = end;
q2sumA = 0;
q2sumB = 0;
ener = 0;
if (mdatoms->nChargePerturbed == 0) {
for(i=start; i<niat; i++) {
qiA = chargeA[i];
if (i < end)
q2sumA += qiA*qiA;
/* Do the exclusions */
j1 = excl->index[i];
j2 = excl->index[i+1];
for(j=j1; j<j2; j++) {
k = AA[j];
if (k > i) {
qqA = qiA*chargeA[k];
if (qqA != 0) {
if (g) {
rvec_sub(x[i],x[k],dx);
ivec_sub(SHIFT_IVEC(g,i),SHIFT_IVEC(g,k),dt);
ki=IVEC2IS(dt);
} else if (bMolPBC) {
ki = pbc_dx_aiuc(pbc,x[i],x[k],dx);
} else
rvec_sub(x[i],x[k],dx);
ener += qqA*(ek*norm2(dx) - ec);
svmul(-2*qqA*ek,dx,df);
rvec_inc(f[i],df);
rvec_dec(f[k],df);
rvec_inc(fshift[ki],df);
rvec_dec(fshift[CENTRAL],df);
}
}
}
}
ener += -0.5*ec*q2sumA;
} else {
L1 = 1.0 - lambda;
for(i=start; i<niat; i++) {
qiA = chargeA[i];
qiB = chargeB[i];
if (i < end) {
q2sumA += qiA*qiA;
q2sumB += qiB*qiB;
}
/* Do the exclusions */
j1 = excl->index[i];
j2 = excl->index[i+1];
for(j=j1; j<j2; j++) {
k = AA[j];
if (k > i) {
qqA = qiA*chargeA[k];
qqB = qiB*chargeB[k];
if (qqA != 0 || qqB != 0) {
qqL = L1*qqA + lambda*qqB;
if (g) {
rvec_sub(x[i],x[k],dx);
ivec_sub(SHIFT_IVEC(g,i),SHIFT_IVEC(g,k),dt);
ki=IVEC2IS(dt);
} else if (bMolPBC) {
ki = pbc_dx_aiuc(pbc,x[i],x[k],dx);
} else
rvec_sub(x[i],x[k],dx);
v = ek*norm2(dx) - ec;
ener += qqL*v;
svmul(-2*qqL*ek,dx,df);
rvec_inc(f[i],df);
rvec_dec(f[k],df);
rvec_inc(fshift[ki],df);
rvec_dec(fshift[CENTRAL],df);
*dvdlambda += (qqB - qqA)*v;
}
}
}
}
ener += -0.5*ec*(L1*q2sumA + lambda*q2sumB);
*dvdlambda += -0.5*ec*(q2sumB - q2sumA);
}
if (debug)
fprintf(debug,"RF exclusion energy: %g\n",ener);
return ener;
}
void init_orires(FILE *fplog,const gmx_mtop_t *mtop,
rvec xref[],
const t_inputrec *ir,
const gmx_multisim_t *ms,t_oriresdata *od,
t_state *state)
{
int i,j,d,ex,nmol,nr,*nr_ex;
double mtot;
rvec com;
gmx_mtop_ilistloop_t iloop;
t_ilist *il;
gmx_mtop_atomloop_all_t aloop;
t_atom *atom;
od->fc = ir->orires_fc;
od->nex = 0;
od->S = NULL;
od->nr = gmx_mtop_ftype_count(mtop,F_ORIRES);
if (od->nr == 0)
{
return;
}
nr_ex = NULL;
iloop = gmx_mtop_ilistloop_init(mtop);
while (gmx_mtop_ilistloop_next(iloop,&il,&nmol))
{
for(i=0; i<il[F_ORIRES].nr; i+=3)
{
ex = mtop->ffparams.iparams[il[F_ORIRES].iatoms[i]].orires.ex;
if (ex >= od->nex)
{
srenew(nr_ex,ex+1);
for(j=od->nex; j<ex+1; j++)
{
nr_ex[j] = 0;
}
od->nex = ex+1;
}
nr_ex[ex]++;
}
}
snew(od->S,od->nex);
/* When not doing time averaging, the instaneous and time averaged data
* are indentical and the pointers can point to the same memory.
*/
snew(od->Dinsl,od->nr);
if (ms)
{
snew(od->Dins,od->nr);
}
else
{
od->Dins = od->Dinsl;
}
if (ir->orires_tau == 0)
{
od->Dtav = od->Dins;
od->edt = 0.0;
od->edt1 = 1.0;
}
else
{
snew(od->Dtav,od->nr);
od->edt = exp(-ir->delta_t/ir->orires_tau);
od->edt1 = 1.0 - od->edt;
/* Extend the state with the orires history */
state->flags |= (1<<estORIRE_INITF);
state->hist.orire_initf = 1;
state->flags |= (1<<estORIRE_DTAV);
state->hist.norire_Dtav = od->nr*5;
snew(state->hist.orire_Dtav,state->hist.norire_Dtav);
}
snew(od->oinsl,od->nr);
if (ms)
{
snew(od->oins,od->nr);
}
else
{
od->oins = od->oinsl;
}
if (ir->orires_tau == 0) {
od->otav = od->oins;
}
else
{
snew(od->otav,od->nr);
}
snew(od->tmp,od->nex);
snew(od->TMP,od->nex);
for(ex=0; ex<od->nex; ex++)
{
snew(od->TMP[ex],5);
for(i=0; i<5; i++)
{
snew(od->TMP[ex][i],5);
}
}
od->nref = 0;
for(i=0; i<mtop->natoms; i++)
{
if (ggrpnr(&mtop->groups,egcORFIT,i) == 0)
{
od->nref++;
}
}
snew(od->mref,od->nref);
snew(od->xref,od->nref);
snew(od->xtmp,od->nref);
snew(od->eig,od->nex*12);
/* Determine the reference structure on the master node.
* Copy it to the other nodes after checking multi compatibility,
* so we are sure the subsystems match before copying.
*/
clear_rvec(com);
mtot = 0.0;
j = 0;
aloop = gmx_mtop_atomloop_all_init(mtop);
while(gmx_mtop_atomloop_all_next(aloop,&i,&atom))
{
if (mtop->groups.grpnr[egcORFIT] == NULL ||
mtop->groups.grpnr[egcORFIT][i] == 0)
{
/* Not correct for free-energy with changing masses */
od->mref[j] = atom->m;
if (ms==NULL || MASTERSIM(ms))
{
copy_rvec(xref[i],od->xref[j]);
for(d=0; d<DIM; d++)
{
com[d] += od->mref[j]*xref[i][d];
}
}
mtot += od->mref[j];
j++;
}
}
svmul(1.0/mtot,com,com);
if (ms==NULL || MASTERSIM(ms))
{
for(j=0; j<od->nref; j++)
{
rvec_dec(od->xref[j],com);
}
}
fprintf(fplog,"Found %d orientation experiments\n",od->nex);
for(i=0; i<od->nex; i++)
{
fprintf(fplog," experiment %d has %d restraints\n",i+1,nr_ex[i]);
}
sfree(nr_ex);
fprintf(fplog," the fit group consists of %d atoms and has total mass %g\n",
od->nref,mtot);
if (ms)
{
fprintf(fplog," the orientation restraints are ensemble averaged over %d systems\n",ms->nsim);
check_multi_int(fplog,ms,od->nr,
"the number of orientation restraints");
check_multi_int(fplog,ms,od->nref,
"the number of fit atoms for orientation restraining");
check_multi_int(fplog,ms,ir->nsteps,"nsteps");
/* Copy the reference coordinates from the master to the other nodes */
gmx_sum_sim(DIM*od->nref,od->xref[0],ms);
}
please_cite(fplog,"Hess2003");
}
static void list_trn(char *fn)
{
static real mass[5] = { 15.9994, 1.008, 1.008, 0.0, 0.0 };
int i,j=0,m,fpread,fpwrite,nframe;
rvec *x,*v,*f,fmol[2],xcm[2],torque[j],dx;
real mmm,len;
matrix box;
t_trnheader trn;
gmx_bool bOK;
printf("Going to open %s\n",fn);
fpread = open_trn(fn,"r");
fpwrite = open_tpx(NULL,"w");
gmx_fio_setdebug(fpwrite,TRUE);
mmm=mass[0]+2*mass[1];
for(i=0; (i<5); i++)
mass[i] /= mmm;
nframe = 0;
while (fread_trnheader(fpread,&trn,&bOK)) {
snew(x,trn.natoms);
snew(v,trn.natoms);
snew(f,trn.natoms);
if (fread_htrn(fpread,&trn,
trn.box_size ? box : NULL,
trn.x_size ? x : NULL,
trn.v_size ? v : NULL,
trn.f_size ? f : NULL)) {
if (trn.x_size && trn.f_size) {
printf("There are %d atoms\n",trn.natoms);
for(j=0; (j<2); j++) {
clear_rvec(xcm[j]);
clear_rvec(fmol[j]);
clear_rvec(torque[j]);
for(i=5*j; (i<5*j+5); i++) {
rvec_inc(fmol[j],f[i]);
for(m=0; (m<DIM); m++)
xcm[j][m] += mass[i%5]*x[i][m];
}
for(i=5*j; (i<5*j+5); i++) {
rvec_dec(x[i],xcm[j]);
cprod(x[i],f[i],dx);
rvec_inc(torque[j],dx);
rvec_inc(x[i],xcm[j]);
}
}
pr_rvecs(stdout,0,"FMOL ",fmol,2);
pr_rvecs(stdout,0,"TORQUE",torque,2);
printf("Distance matrix Water1-Water2\n%5s","");
for(j=0; (j<5); j++)
printf(" %10s",nm[j]);
printf("\n");
for(j=0; (j<5); j++) {
printf("%5s",nm[j]);
for(i=5; (i<10); i++) {
rvec_sub(x[i],x[j],dx);
len = sqrt(iprod(dx,dx));
printf(" %10.7f",len);
}
printf("\n");
}
}
}
sfree(x);
sfree(v);
sfree(f);
nframe++;
}
if (!bOK)
fprintf(stderr,"\nWARNING: Incomplete frame header: nr %d, t=%g\n",
nframe,trn.t);
close_tpx(fpwrite);
close_trn(fpread);
}
real calc_orires_dev(const gmx_multisim_t *ms,
int nfa,const t_iatom forceatoms[],const t_iparams ip[],
const t_mdatoms *md,const rvec x[],const t_pbc *pbc,
t_fcdata *fcd,history_t *hist)
{
int fa,d,i,j,type,ex,nref;
real edt,edt1,invn,pfac,r2,invr,corrfac,weight,wsv2,sw,dev;
tensor *S,R,TMP;
rvec5 *Dinsl,*Dins,*Dtav,*rhs;
real *mref,***T;
double mtot;
rvec *xref,*xtmp,com,r_unrot,r;
t_oriresdata *od;
bool bTAV;
const real two_thr=2.0/3.0;
od = &(fcd->orires);
if (od->nr == 0)
{
/* This means that this is not the master node */
gmx_fatal(FARGS,"Orientation restraints are only supported on the master node, use less processors");
}
bTAV = (od->edt != 0);
edt = od->edt;
edt1 = od->edt1;
S = od->S;
Dinsl= od->Dinsl;
Dins = od->Dins;
Dtav = od->Dtav;
T = od->TMP;
rhs = od->tmp;
nref = od->nref;
mref = od->mref;
xref = od->xref;
xtmp = od->xtmp;
if (bTAV)
{
od->exp_min_t_tau = hist->orire_initf*edt;
/* Correction factor to correct for the lack of history
* at short times.
*/
corrfac = 1.0/(1.0 - od->exp_min_t_tau);
}
else
{
corrfac = 1.0;
}
if (ms)
{
invn = 1.0/ms->nsim;
}
else
{
invn = 1.0;
}
clear_rvec(com);
mtot = 0;
j=0;
for(i=0; i<md->nr; i++)
{
if (md->cORF[i] == 0)
{
copy_rvec(x[i],xtmp[j]);
mref[j] = md->massT[i];
for(d=0; d<DIM; d++)
{
com[d] += mref[j]*xref[j][d];
}
mtot += mref[j];
j++;
}
}
svmul(1.0/mtot,com,com);
for(j=0; j<nref; j++)
{
rvec_dec(xtmp[j],com);
}
/* Calculate the rotation matrix to rotate x to the reference orientation */
calc_fit_R(DIM,nref,mref,xref,xtmp,R);
copy_mat(R,od->R);
d = 0;
for(fa=0; fa<nfa; fa+=3)
{
type = forceatoms[fa];
if (pbc)
{
pbc_dx_aiuc(pbc,x[forceatoms[fa+1]],x[forceatoms[fa+2]],r_unrot);
}
else
{
rvec_sub(x[forceatoms[fa+1]],x[forceatoms[fa+2]],r_unrot);
}
mvmul(R,r_unrot,r);
r2 = norm2(r);
invr = invsqrt(r2);
/* Calculate the prefactor for the D tensor, this includes the factor 3! */
pfac = ip[type].orires.c*invr*invr*3;
for(i=0; i<ip[type].orires.power; i++)
{
pfac *= invr;
}
Dinsl[d][0] = pfac*(2*r[0]*r[0] + r[1]*r[1] - r2);
Dinsl[d][1] = pfac*(2*r[0]*r[1]);
Dinsl[d][2] = pfac*(2*r[0]*r[2]);
Dinsl[d][3] = pfac*(2*r[1]*r[1] + r[0]*r[0] - r2);
Dinsl[d][4] = pfac*(2*r[1]*r[2]);
if (ms)
{
for(i=0; i<5; i++)
{
Dins[d][i] = Dinsl[d][i]*invn;
}
}
d++;
}
if (ms)
{
gmx_sum_sim(5*od->nr,Dins[0],ms);
}
/* Calculate the order tensor S for each experiment via optimization */
for(ex=0; ex<od->nex; ex++)
{
for(i=0; i<5; i++)
{
rhs[ex][i] = 0;
for(j=0; j<=i; j++)
{
T[ex][i][j] = 0;
}
}
}
d = 0;
for(fa=0; fa<nfa; fa+=3)
{
if (bTAV)
{
/* Here we update Dtav in t_fcdata using the data in history_t.
* Thus the results stay correct when this routine
* is called multiple times.
*/
for(i=0; i<5; i++)
{
Dtav[d][i] = edt*hist->orire_Dtav[d*5+i] + edt1*Dins[d][i];
}
}
type = forceatoms[fa];
ex = ip[type].orires.ex;
weight = ip[type].orires.kfac;
/* Calculate the vector rhs and half the matrix T for the 5 equations */
for(i=0; i<5; i++) {
rhs[ex][i] += Dtav[d][i]*ip[type].orires.obs*weight;
for(j=0; j<=i; j++)
{
T[ex][i][j] += Dtav[d][i]*Dtav[d][j]*weight;
}
}
d++;
}
/* Now we have all the data we can calculate S */
for(ex=0; ex<od->nex; ex++)
{
/* Correct corrfac and copy one half of T to the other half */
for(i=0; i<5; i++)
{
rhs[ex][i] *= corrfac;
T[ex][i][i] *= sqr(corrfac);
for(j=0; j<i; j++)
{
T[ex][i][j] *= sqr(corrfac);
T[ex][j][i] = T[ex][i][j];
}
}
m_inv_gen(T[ex],5,T[ex]);
/* Calculate the orientation tensor S for this experiment */
S[ex][0][0] = 0;
S[ex][0][1] = 0;
S[ex][0][2] = 0;
S[ex][1][1] = 0;
S[ex][1][2] = 0;
for(i=0; i<5; i++)
{
S[ex][0][0] += 1.5*T[ex][0][i]*rhs[ex][i];
S[ex][0][1] += 1.5*T[ex][1][i]*rhs[ex][i];
S[ex][0][2] += 1.5*T[ex][2][i]*rhs[ex][i];
S[ex][1][1] += 1.5*T[ex][3][i]*rhs[ex][i];
S[ex][1][2] += 1.5*T[ex][4][i]*rhs[ex][i];
}
S[ex][1][0] = S[ex][0][1];
S[ex][2][0] = S[ex][0][2];
S[ex][2][1] = S[ex][1][2];
S[ex][2][2] = -S[ex][0][0] - S[ex][1][1];
}
wsv2 = 0;
sw = 0;
d = 0;
for(fa=0; fa<nfa; fa+=3)
{
type = forceatoms[fa];
ex = ip[type].orires.ex;
od->otav[d] = two_thr*
corrfac*(S[ex][0][0]*Dtav[d][0] + S[ex][0][1]*Dtav[d][1] +
S[ex][0][2]*Dtav[d][2] + S[ex][1][1]*Dtav[d][3] +
S[ex][1][2]*Dtav[d][4]);
if (bTAV)
{
od->oins[d] = two_thr*(S[ex][0][0]*Dins[d][0] + S[ex][0][1]*Dins[d][1] +
S[ex][0][2]*Dins[d][2] + S[ex][1][1]*Dins[d][3] +
S[ex][1][2]*Dins[d][4]);
}
if (ms)
{
/* When ensemble averaging is used recalculate the local orientation
* for output to the energy file.
*/
od->oinsl[d] = two_thr*
(S[ex][0][0]*Dinsl[d][0] + S[ex][0][1]*Dinsl[d][1] +
S[ex][0][2]*Dinsl[d][2] + S[ex][1][1]*Dinsl[d][3] +
S[ex][1][2]*Dinsl[d][4]);
}
dev = od->otav[d] - ip[type].orires.obs;
wsv2 += ip[type].orires.kfac*sqr(dev);
sw += ip[type].orires.kfac;
d++;
}
od->rmsdev = sqrt(wsv2/sw);
/* Rotate the S matrices back, so we get the correct grad(tr(S D)) */
for(ex=0; ex<od->nex; ex++)
{
tmmul(R,S[ex],TMP);
mmul(TMP,R,S[ex]);
}
return od->rmsdev;
/* Approx. 120*nfa/3 flops */
}
/* There's nothing special to do here if just masses are perturbed,
* but if either charge or type is perturbed then the implementation
* requires that B states are defined for both charge and type, and
* does not optimize for the cases where only one changes.
*
* The parameter vectors for B states are left undefined in atoms2md()
* when either FEP is inactive, or when there are no mass/charge/type
* perturbations. The parameter vectors for LJ-PME are likewise
* undefined when LJ-PME is not active. This works because
* bHaveChargeOrTypePerturbed handles the control flow. */
void ewald_LRcorrection(int numAtomsLocal,
t_commrec *cr,
int numThreads, int thread,
t_forcerec *fr,
real *chargeA, real *chargeB,
real *C6A, real *C6B,
real *sigmaA, real *sigmaB,
real *sigma3A, real *sigma3B,
gmx_bool bHaveChargeOrTypePerturbed,
gmx_bool calc_excl_corr,
t_blocka *excl, rvec x[],
matrix box, rvec mu_tot[],
int ewald_geometry, real epsilon_surface,
rvec *f, tensor vir_q, tensor vir_lj,
real *Vcorr_q, real *Vcorr_lj,
real lambda_q, real lambda_lj,
real *dvdlambda_q, real *dvdlambda_lj)
{
int numAtomsToBeCorrected;
if (calc_excl_corr)
{
/* We need to correct all exclusion pairs (cutoff-scheme = group) */
numAtomsToBeCorrected = excl->nr;
GMX_RELEASE_ASSERT(numAtomsToBeCorrected >= numAtomsLocal, "We might need to do self-corrections");
}
else
{
/* We need to correct only self interactions */
numAtomsToBeCorrected = numAtomsLocal;
}
int start = (numAtomsToBeCorrected* thread )/numThreads;
int end = (numAtomsToBeCorrected*(thread + 1))/numThreads;
int i, i1, i2, j, k, m, iv, jv, q;
int *AA;
double Vexcl_q, dvdl_excl_q, dvdl_excl_lj; /* Necessary for precision */
double Vexcl_lj;
real one_4pi_eps;
real v, vc, qiA, qiB, dr2, rinv;
real Vself_q[2], Vself_lj[2], Vdipole[2], rinv2, ewc_q = fr->ewaldcoeff_q, ewcdr;
real ewc_lj = fr->ewaldcoeff_lj, ewc_lj2 = ewc_lj * ewc_lj;
real c6Ai = 0, c6Bi = 0, c6A = 0, c6B = 0, ewcdr2, ewcdr4, c6L = 0, rinv6;
rvec df, dx, mutot[2], dipcorrA, dipcorrB;
tensor dxdf_q = {{0}}, dxdf_lj = {{0}};
real vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
real L1_q, L1_lj, dipole_coeff, qqA, qqB, qqL, vr0_q, vr0_lj = 0;
gmx_bool bMolPBC = fr->bMolPBC;
gmx_bool bDoingLBRule = (fr->ljpme_combination_rule == eljpmeLB);
gmx_bool bNeedLongRangeCorrection;
/* This routine can be made faster by using tables instead of analytical interactions
* However, that requires a thorough verification that they are correct in all cases.
*/
one_4pi_eps = ONE_4PI_EPS0/fr->epsilon_r;
vr0_q = ewc_q*M_2_SQRTPI;
if (EVDW_PME(fr->vdwtype))
{
vr0_lj = -gmx::power6(ewc_lj)/6.0;
}
AA = excl->a;
Vexcl_q = 0;
Vexcl_lj = 0;
dvdl_excl_q = 0;
dvdl_excl_lj = 0;
Vdipole[0] = 0;
Vdipole[1] = 0;
L1_q = 1.0-lambda_q;
L1_lj = 1.0-lambda_lj;
/* Note that we have to transform back to gromacs units, since
* mu_tot contains the dipole in debye units (for output).
*/
for (i = 0; (i < DIM); i++)
{
mutot[0][i] = mu_tot[0][i]*DEBYE2ENM;
mutot[1][i] = mu_tot[1][i]*DEBYE2ENM;
dipcorrA[i] = 0;
dipcorrB[i] = 0;
}
dipole_coeff = 0;
switch (ewald_geometry)
{
case eewg3D:
if (epsilon_surface != 0)
{
dipole_coeff =
2*M_PI*ONE_4PI_EPS0/((2*epsilon_surface + fr->epsilon_r)*vol);
for (i = 0; (i < DIM); i++)
{
dipcorrA[i] = 2*dipole_coeff*mutot[0][i];
dipcorrB[i] = 2*dipole_coeff*mutot[1][i];
}
}
break;
case eewg3DC:
dipole_coeff = 2*M_PI*one_4pi_eps/vol;
dipcorrA[ZZ] = 2*dipole_coeff*mutot[0][ZZ];
dipcorrB[ZZ] = 2*dipole_coeff*mutot[1][ZZ];
break;
default:
gmx_incons("Unsupported Ewald geometry");
break;
}
if (debug)
{
fprintf(debug, "dipcorr = %8.3f %8.3f %8.3f\n",
dipcorrA[XX], dipcorrA[YY], dipcorrA[ZZ]);
fprintf(debug, "mutot = %8.3f %8.3f %8.3f\n",
mutot[0][XX], mutot[0][YY], mutot[0][ZZ]);
}
bNeedLongRangeCorrection = (calc_excl_corr || dipole_coeff != 0);
if (bNeedLongRangeCorrection && !bHaveChargeOrTypePerturbed)
{
for (i = start; (i < end); i++)
{
/* Initiate local variables (for this i-particle) to 0 */
qiA = chargeA[i]*one_4pi_eps;
if (EVDW_PME(fr->vdwtype))
{
c6Ai = C6A[i];
if (bDoingLBRule)
{
c6Ai *= sigma3A[i];
}
}
if (calc_excl_corr)
{
i1 = excl->index[i];
i2 = excl->index[i+1];
/* Loop over excluded neighbours */
for (j = i1; (j < i2); j++)
{
k = AA[j];
/*
* First we must test whether k <> i, and then,
* because the exclusions are all listed twice i->k
* and k->i we must select just one of the two. As
* a minor optimization we only compute forces when
* the charges are non-zero.
*/
if (k > i)
{
qqA = qiA*chargeA[k];
if (EVDW_PME(fr->vdwtype))
{
c6A = c6Ai * C6A[k];
if (bDoingLBRule)
{
c6A *= gmx::power6(0.5*(sigmaA[i]+sigmaA[k]))*sigma3A[k];
}
}
if (qqA != 0.0 || c6A != 0.0)
{
rvec_sub(x[i], x[k], dx);
if (bMolPBC)
{
/* Cheap pbc_dx, assume excluded pairs are at short distance. */
for (m = DIM-1; (m >= 0); m--)
{
if (dx[m] > 0.5*box[m][m])
{
rvec_dec(dx, box[m]);
}
else if (dx[m] < -0.5*box[m][m])
{
rvec_inc(dx, box[m]);
}
}
}
dr2 = norm2(dx);
/* Distance between two excluded particles
* may be zero in the case of shells
*/
if (dr2 != 0)
{
rinv = gmx::invsqrt(dr2);
rinv2 = rinv*rinv;
if (qqA != 0.0)
{
real dr, fscal;
dr = 1.0/rinv;
ewcdr = ewc_q*dr;
vc = qqA*std::erf(ewcdr)*rinv;
Vexcl_q += vc;
#if GMX_DOUBLE
/* Relative accuracy at R_ERF_R_INACC of 3e-10 */
#define R_ERF_R_INACC 0.006
#else
/* Relative accuracy at R_ERF_R_INACC of 2e-5 */
#define R_ERF_R_INACC 0.1
#endif
/* fscal is the scalar force pre-multiplied by rinv,
* to normalise the relative position vector dx */
if (ewcdr > R_ERF_R_INACC)
{
fscal = rinv2*(vc - qqA*ewc_q*M_2_SQRTPI*exp(-ewcdr*ewcdr));
}
else
{
/* Use a fourth order series expansion for small ewcdr */
fscal = ewc_q*ewc_q*qqA*vr0_q*(2.0/3.0 - 0.4*ewcdr*ewcdr);
}
/* The force vector is obtained by multiplication with
* the relative position vector
*/
svmul(fscal, dx, df);
rvec_inc(f[k], df);
rvec_dec(f[i], df);
for (iv = 0; (iv < DIM); iv++)
{
for (jv = 0; (jv < DIM); jv++)
{
dxdf_q[iv][jv] += dx[iv]*df[jv];
}
}
}
if (c6A != 0.0)
{
real fscal;
rinv6 = rinv2*rinv2*rinv2;
ewcdr2 = ewc_lj2*dr2;
ewcdr4 = ewcdr2*ewcdr2;
/* We get the excluded long-range contribution from -C6*(1-g(r))
* g(r) is also defined in the manual under LJ-PME
*/
vc = -c6A*rinv6*(1.0 - exp(-ewcdr2)*(1 + ewcdr2 + 0.5*ewcdr4));
Vexcl_lj += vc;
/* The force is the derivative of the potential vc.
* fscal is the scalar force pre-multiplied by rinv,
* to normalise the relative position vector dx */
fscal = 6.0*vc*rinv2 + c6A*rinv6*exp(-ewcdr2)*ewc_lj2*ewcdr4;
/* The force vector is obtained by multiplication with
* the relative position vector
*/
svmul(fscal, dx, df);
rvec_inc(f[k], df);
rvec_dec(f[i], df);
for (iv = 0; (iv < DIM); iv++)
{
for (jv = 0; (jv < DIM); jv++)
{
dxdf_lj[iv][jv] += dx[iv]*df[jv];
}
}
}
}
else
{
Vexcl_q += qqA*vr0_q;
Vexcl_lj += c6A*vr0_lj;
}
}
}
}
}
/* Dipole correction on force */
if (dipole_coeff != 0 && i < numAtomsLocal)
{
for (j = 0; (j < DIM); j++)
{
f[i][j] -= dipcorrA[j]*chargeA[i];
}
}
}
}
else if (bNeedLongRangeCorrection)
{
for (i = start; (i < end); i++)
{
/* Initiate local variables (for this i-particle) to 0 */
qiA = chargeA[i]*one_4pi_eps;
qiB = chargeB[i]*one_4pi_eps;
if (EVDW_PME(fr->vdwtype))
{
c6Ai = C6A[i];
c6Bi = C6B[i];
if (bDoingLBRule)
{
c6Ai *= sigma3A[i];
c6Bi *= sigma3B[i];
}
}
if (calc_excl_corr)
{
i1 = excl->index[i];
i2 = excl->index[i+1];
/* Loop over excluded neighbours */
for (j = i1; (j < i2); j++)
{
k = AA[j];
if (k > i)
{
qqA = qiA*chargeA[k];
qqB = qiB*chargeB[k];
if (EVDW_PME(fr->vdwtype))
{
c6A = c6Ai*C6A[k];
c6B = c6Bi*C6B[k];
if (bDoingLBRule)
{
c6A *= gmx::power6(0.5*(sigmaA[i]+sigmaA[k]))*sigma3A[k];
c6B *= gmx::power6(0.5*(sigmaB[i]+sigmaB[k]))*sigma3B[k];
}
}
if (qqA != 0.0 || qqB != 0.0 || c6A != 0.0 || c6B != 0.0)
{
real fscal;
qqL = L1_q*qqA + lambda_q*qqB;
if (EVDW_PME(fr->vdwtype))
{
c6L = L1_lj*c6A + lambda_lj*c6B;
}
rvec_sub(x[i], x[k], dx);
if (bMolPBC)
{
/* Cheap pbc_dx, assume excluded pairs are at short distance. */
for (m = DIM-1; (m >= 0); m--)
{
if (dx[m] > 0.5*box[m][m])
{
rvec_dec(dx, box[m]);
}
else if (dx[m] < -0.5*box[m][m])
{
rvec_inc(dx, box[m]);
}
}
}
dr2 = norm2(dx);
if (dr2 != 0)
{
rinv = gmx::invsqrt(dr2);
rinv2 = rinv*rinv;
if (qqA != 0.0 || qqB != 0.0)
{
real dr;
dr = 1.0/rinv;
v = std::erf(ewc_q*dr)*rinv;
vc = qqL*v;
Vexcl_q += vc;
/* fscal is the scalar force pre-multiplied by rinv,
* to normalise the relative position vector dx */
fscal = rinv2*(vc-qqL*ewc_q*M_2_SQRTPI*exp(-ewc_q*ewc_q*dr2));
dvdl_excl_q += (qqB - qqA)*v;
/* The force vector is obtained by multiplication with
* the relative position vector
*/
svmul(fscal, dx, df);
rvec_inc(f[k], df);
rvec_dec(f[i], df);
for (iv = 0; (iv < DIM); iv++)
{
for (jv = 0; (jv < DIM); jv++)
{
dxdf_q[iv][jv] += dx[iv]*df[jv];
}
}
}
if ((c6A != 0.0 || c6B != 0.0) && EVDW_PME(fr->vdwtype))
{
rinv6 = rinv2*rinv2*rinv2;
ewcdr2 = ewc_lj2*dr2;
ewcdr4 = ewcdr2*ewcdr2;
v = -rinv6*(1.0 - exp(-ewcdr2)*(1 + ewcdr2 + 0.5*ewcdr4));
vc = c6L*v;
Vexcl_lj += vc;
/* fscal is the scalar force pre-multiplied by rinv,
* to normalise the relative position vector dx */
fscal = 6.0*vc*rinv2 + c6L*rinv6*exp(-ewcdr2)*ewc_lj2*ewcdr4;
dvdl_excl_lj += (c6B - c6A)*v;
/* The force vector is obtained by multiplication with
* the relative position vector
*/
svmul(fscal, dx, df);
rvec_inc(f[k], df);
rvec_dec(f[i], df);
for (iv = 0; (iv < DIM); iv++)
{
for (jv = 0; (jv < DIM); jv++)
{
dxdf_lj[iv][jv] += dx[iv]*df[jv];
}
}
}
}
else
{
Vexcl_q += qqL*vr0_q;
dvdl_excl_q += (qqB - qqA)*vr0_q;
Vexcl_lj += c6L*vr0_lj;
dvdl_excl_lj += (c6B - c6A)*vr0_lj;
}
}
}
}
}
/* Dipole correction on force */
if (dipole_coeff != 0 && i < numAtomsLocal)
{
for (j = 0; (j < DIM); j++)
{
f[i][j] -= L1_q*dipcorrA[j]*chargeA[i]
+ lambda_q*dipcorrB[j]*chargeB[i];
}
}
}
}
for (iv = 0; (iv < DIM); iv++)
{
for (jv = 0; (jv < DIM); jv++)
{
vir_q[iv][jv] += 0.5*dxdf_q[iv][jv];
vir_lj[iv][jv] += 0.5*dxdf_lj[iv][jv];
}
}
Vself_q[0] = 0;
Vself_q[1] = 0;
Vself_lj[0] = 0;
Vself_lj[1] = 0;
/* Global corrections only on master process */
if (MASTER(cr) && thread == 0)
{
for (q = 0; q < (bHaveChargeOrTypePerturbed ? 2 : 1); q++)
{
if (calc_excl_corr)
{
/* Self-energy correction */
Vself_q[q] = ewc_q*one_4pi_eps*fr->q2sum[q]*M_1_SQRTPI;
if (EVDW_PME(fr->vdwtype))
{
Vself_lj[q] = fr->c6sum[q]*0.5*vr0_lj;
}
}
/* Apply surface dipole correction:
* correction = dipole_coeff * (dipole)^2
*/
if (dipole_coeff != 0)
{
if (ewald_geometry == eewg3D)
{
Vdipole[q] = dipole_coeff*iprod(mutot[q], mutot[q]);
}
else if (ewald_geometry == eewg3DC)
{
Vdipole[q] = dipole_coeff*mutot[q][ZZ]*mutot[q][ZZ];
}
}
}
}
if (!bHaveChargeOrTypePerturbed)
{
*Vcorr_q = Vdipole[0] - Vself_q[0] - Vexcl_q;
if (EVDW_PME(fr->vdwtype))
{
*Vcorr_lj = -Vself_lj[0] - Vexcl_lj;
}
}
else
{
*Vcorr_q = L1_q*(Vdipole[0] - Vself_q[0])
+ lambda_q*(Vdipole[1] - Vself_q[1])
- Vexcl_q;
*dvdlambda_q += Vdipole[1] - Vself_q[1]
- (Vdipole[0] - Vself_q[0]) - dvdl_excl_q;
if (EVDW_PME(fr->vdwtype))
{
*Vcorr_lj = -(L1_lj*Vself_lj[0] + lambda_lj*Vself_lj[1]) - Vexcl_lj;
*dvdlambda_lj += -Vself_lj[1] + Vself_lj[0] - dvdl_excl_lj;
}
}
if (debug)
{
fprintf(debug, "Long Range corrections for Ewald interactions:\n");
fprintf(debug, "q2sum = %g, Vself_q=%g c6sum = %g, Vself_lj=%g\n",
L1_q*fr->q2sum[0]+lambda_q*fr->q2sum[1], L1_q*Vself_q[0]+lambda_q*Vself_q[1], L1_lj*fr->c6sum[0]+lambda_lj*fr->c6sum[1], L1_lj*Vself_lj[0]+lambda_lj*Vself_lj[1]);
fprintf(debug, "Electrostatic Long Range correction: Vexcl=%g\n", Vexcl_q);
fprintf(debug, "Lennard-Jones Long Range correction: Vexcl=%g\n", Vexcl_lj);
if (MASTER(cr) && thread == 0)
{
if (epsilon_surface > 0 || ewald_geometry == eewg3DC)
{
fprintf(debug, "Total dipole correction: Vdipole=%g\n",
L1_q*Vdipole[0]+lambda_q*Vdipole[1]);
}
}
}
}
int gmx_vanhove(int argc,char *argv[])
{
const char *desc[] = {
"g_vanhove computes the Van Hove correlation function.",
"The Van Hove G(r,t) is the probability that a particle that is at r0",
"at time zero can be found at position r0+r at time t.",
"g_vanhove determines G not for a vector r, but for the length of r.",
"Thus it gives the probability that a particle moves a distance of r",
"in time t.",
"Jumps across the periodic boundaries are removed.",
"Corrections are made for scaling due to isotropic",
"or anisotropic pressure coupling.",
"[PAR]",
"With option [TT]-om[tt] the whole matrix can be written as a function",
"of t and r or as a function of sqrt(t) and r (option [TT]-sqrt[tt]).",
"[PAR]",
"With option [TT]-or[tt] the Van Hove function is plotted for one",
"or more values of t. Option [TT]-nr[tt] sets the number of times,",
"option [TT]-fr[tt] the number spacing between the times.",
"The binwidth is set with option [TT]-rbin[tt]. The number of bins",
"is determined automatically.",
"[PAR]",
"With option [TT]-ot[tt] the integral up to a certain distance",
"(option [TT]-rt[tt]) is plotted as a function of time.",
"[PAR]",
"For all frames that are read the coordinates of the selected particles",
"are stored in memory. Therefore the program may use a lot of memory.",
"For options [TT]-om[tt] and [TT]-ot[tt] the program may be slow.",
"This is because the calculation scales as the number of frames times",
"[TT]-fm[tt] or [TT]-ft[tt].",
"Note that with the [TT]-dt[tt] option the memory usage and calculation",
"time can be reduced."
};
static int fmmax=0,ftmax=0,nlev=81,nr=1,fshift=0;
static real sbin=0,rmax=2,rbin=0.01,mmax=0,rint=0;
t_pargs pa[] = {
{ "-sqrt", FALSE, etREAL,{&sbin},
"Use sqrt(t) on the matrix axis which binspacing # in sqrt(ps)" },
{ "-fm", FALSE, etINT, {&fmmax},
"Number of frames in the matrix, 0 is plot all" },
{ "-rmax", FALSE, etREAL, {&rmax},
"Maximum r in the matrix (nm)" },
{ "-rbin", FALSE, etREAL, {&rbin},
"Binwidth in the matrix and for -or (nm)" },
{ "-mmax", FALSE, etREAL, {&mmax},
"Maximum density in the matrix, 0 is calculate (1/nm)" },
{ "-nlevels" ,FALSE, etINT, {&nlev},
"Number of levels in the matrix" },
{ "-nr", FALSE, etINT, {&nr},
"Number of curves for the -or output" },
{ "-fr", FALSE, etINT, {&fshift},
"Frame spacing for the -or output" },
{ "-rt", FALSE, etREAL, {&rint},
"Integration limit for the -ot output (nm)" },
{ "-ft", FALSE, etINT, {&ftmax},
"Number of frames in the -ot output, 0 is plot all" }
};
#define NPA asize(pa)
t_filenm fnm[] = {
{ efTRX, NULL, NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXPM, "-om", "vanhove", ffOPTWR },
{ efXVG, "-or", "vanhove_r", ffOPTWR },
{ efXVG, "-ot", "vanhove_t", ffOPTWR }
};
#define NFILE asize(fnm)
output_env_t oenv;
const char *matfile,*otfile,*orfile;
char title[256];
t_topology top;
int ePBC;
matrix boxtop,box,*sbox,avbox,corr;
rvec *xtop,*x,**sx;
int isize,nalloc,nallocn,natom;
t_trxstatus *status;
atom_id *index;
char *grpname;
int nfr,f,ff,i,m,mat_nx=0,nbin=0,bin,mbin,fbin;
real *time,t,invbin=0,rmax2=0,rint2=0,d2;
real invsbin=0,matmax,normfac,dt,*tickx,*ticky;
char buf[STRLEN],**legend;
real **mat=NULL;
int *pt=NULL,**pr=NULL,*mcount=NULL,*tcount=NULL,*rcount=NULL;
FILE *fp;
t_rgb rlo={1,1,1}, rhi={0,0,0};
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
matfile = opt2fn_null("-om",NFILE,fnm);
if (opt2parg_bSet("-fr",NPA,pa))
orfile = opt2fn("-or",NFILE,fnm);
else
orfile = opt2fn_null("-or",NFILE,fnm);
if (opt2parg_bSet("-rt",NPA,pa))
otfile = opt2fn("-ot",NFILE,fnm);
else
otfile = opt2fn_null("-ot",NFILE,fnm);
if (!matfile && !otfile && !orfile) {
fprintf(stderr,
"For output set one (or more) of the output file options\n");
exit(0);
}
read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&xtop,NULL,boxtop,
FALSE);
get_index(&top.atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&isize,&index,&grpname);
nalloc = 0;
time = NULL;
sbox = NULL;
sx = NULL;
clear_mat(avbox);
natom=read_first_x(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
nfr = 0;
do {
if (nfr >= nalloc) {
nalloc += 100;
srenew(time,nalloc);
srenew(sbox,nalloc);
srenew(sx,nalloc);
}
time[nfr] = t;
copy_mat(box,sbox[nfr]);
/* This assumes that the off-diagonal box elements
* are not affected by jumps across the periodic boundaries.
*/
m_add(avbox,box,avbox);
snew(sx[nfr],isize);
for(i=0; i<isize; i++)
copy_rvec(x[index[i]],sx[nfr][i]);
nfr++;
} while (read_next_x(oenv,status,&t,natom,x,box));
/* clean up */
sfree(x);
close_trj(status);
fprintf(stderr,"Read %d frames\n",nfr);
dt = (time[nfr-1] - time[0])/(nfr - 1);
/* Some ugly rounding to get nice nice times in the output */
dt = (int)(10000.0*dt + 0.5)/10000.0;
invbin = 1.0/rbin;
if (matfile) {
if (fmmax <= 0 || fmmax >= nfr)
fmmax = nfr - 1;
snew(mcount,fmmax);
nbin = (int)(rmax*invbin + 0.5);
if (sbin == 0) {
mat_nx = fmmax + 1;
} else {
invsbin = 1.0/sbin;
mat_nx = sqrt(fmmax*dt)*invsbin + 1;
}
snew(mat,mat_nx);
for(f=0; f<mat_nx; f++)
snew(mat[f],nbin);
rmax2 = sqr(nbin*rbin);
/* Initialize time zero */
mat[0][0] = nfr*isize;
mcount[0] += nfr;
} else {
fmmax = 0;
}
if (orfile) {
snew(pr,nr);
nalloc = 0;
snew(rcount,nr);
}
if (otfile) {
if (ftmax <= 0)
ftmax = nfr - 1;
snew(tcount,ftmax);
snew(pt,nfr);
rint2 = rint*rint;
/* Initialize time zero */
pt[0] = nfr*isize;
tcount[0] += nfr;
} else {
ftmax = 0;
}
msmul(avbox,1.0/nfr,avbox);
for(f=0; f<nfr; f++) {
if (f % 100 == 0)
fprintf(stderr,"\rProcessing frame %d",f);
/* Scale all the configuration to the average box */
m_inv_ur0(sbox[f],corr);
mmul_ur0(avbox,corr,corr);
for(i=0; i<isize; i++) {
mvmul_ur0(corr,sx[f][i],sx[f][i]);
if (f > 0) {
/* Correct for periodic jumps */
for(m=DIM-1; m>=0; m--) {
while(sx[f][i][m] - sx[f-1][i][m] > 0.5*avbox[m][m])
rvec_dec(sx[f][i],avbox[m]);
while(sx[f][i][m] - sx[f-1][i][m] <= -0.5*avbox[m][m])
rvec_inc(sx[f][i],avbox[m]);
}
}
}
for(ff=0; ff<f; ff++) {
fbin = f - ff;
if (fbin <= fmmax || fbin <= ftmax) {
if (sbin == 0)
mbin = fbin;
else
mbin = (int)(sqrt(fbin*dt)*invsbin + 0.5);
for(i=0; i<isize; i++) {
d2 = distance2(sx[f][i],sx[ff][i]);
if (mbin < mat_nx && d2 < rmax2) {
bin = (int)(sqrt(d2)*invbin + 0.5);
if (bin < nbin) {
mat[mbin][bin] += 1;
}
}
if (fbin <= ftmax && d2 <= rint2)
pt[fbin]++;
}
if (matfile)
mcount[mbin]++;
if (otfile)
tcount[fbin]++;
}
}
if (orfile) {
for(fbin=0; fbin<nr; fbin++) {
ff = f - (fbin + 1)*fshift;
if (ff >= 0) {
for(i=0; i<isize; i++) {
d2 = distance2(sx[f][i],sx[ff][i]);
bin = (int)(sqrt(d2)*invbin);
if (bin >= nalloc) {
nallocn = 10*(bin/10) + 11;
for(m=0; m<nr; m++) {
srenew(pr[m],nallocn);
for(i=nalloc; i<nallocn; i++)
pr[m][i] = 0;
}
nalloc = nallocn;
}
pr[fbin][bin]++;
}
rcount[fbin]++;
}
}
}
}
fprintf(stderr,"\n");
if (matfile) {
matmax = 0;
for(f=0; f<mat_nx; f++) {
normfac = 1.0/(mcount[f]*isize*rbin);
for(i=0; i<nbin; i++) {
mat[f][i] *= normfac;
if (mat[f][i] > matmax && (f!=0 || i!=0))
matmax = mat[f][i];
}
}
fprintf(stdout,"Value at (0,0): %.3f, maximum of the rest %.3f\n",
mat[0][0],matmax);
if (mmax > 0)
matmax = mmax;
snew(tickx,mat_nx);
for(f=0; f<mat_nx; f++) {
if (sbin == 0)
tickx[f] = f*dt;
else
tickx[f] = f*sbin;
}
snew(ticky,nbin+1);
for(i=0; i<=nbin; i++)
ticky[i] = i*rbin;
fp = ffopen(matfile,"w");
write_xpm(fp,MAT_SPATIAL_Y,"Van Hove function","G (1/nm)",
sbin==0 ? "time (ps)" : "sqrt(time) (ps^1/2)","r (nm)",
mat_nx,nbin,tickx,ticky,mat,0,matmax,rlo,rhi,&nlev);
ffclose(fp);
}
if (orfile) {
fp = xvgropen(orfile,"Van Hove function","r (nm)","G (nm\\S-1\\N)",oenv);
fprintf(fp,"@ subtitle \"for particles in group %s\"\n",grpname);
snew(legend,nr);
for(fbin=0; fbin<nr; fbin++) {
sprintf(buf,"%g ps",(fbin + 1)*fshift*dt);
legend[fbin] = strdup(buf);
}
xvgr_legend(fp,nr,(const char**)legend,oenv);
for(i=0; i<nalloc; i++) {
fprintf(fp,"%g",i*rbin);
for(fbin=0; fbin<nr; fbin++)
fprintf(fp," %g",
(real)pr[fbin][i]/(rcount[fbin]*isize*rbin*(i==0 ? 0.5 : 1)));
fprintf(fp,"\n");
}
ffclose(fp);
}
if (otfile) {
sprintf(buf,"Probability of moving less than %g nm",rint);
fp = xvgropen(otfile,buf,"t (ps)","",oenv);
fprintf(fp,"@ subtitle \"for particles in group %s\"\n",grpname);
for(f=0; f<=ftmax; f++)
fprintf(fp,"%g %g\n",f*dt,(real)pt[f]/(tcount[f]*isize));
ffclose(fp);
}
do_view(oenv, matfile,NULL);
do_view(oenv, orfile,NULL);
do_view(oenv, otfile,NULL);
thanx(stderr);
return 0;
}
double do_tpi(FILE *fplog, t_commrec *cr,
int nfile, const t_filenm fnm[],
const output_env_t oenv, gmx_bool bVerbose, gmx_bool gmx_unused bCompact,
int gmx_unused nstglobalcomm,
gmx_vsite_t gmx_unused *vsite, gmx_constr_t gmx_unused constr,
int gmx_unused stepout,
t_inputrec *inputrec,
gmx_mtop_t *top_global, t_fcdata *fcd,
t_state *state,
t_mdatoms *mdatoms,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
gmx_edsam_t gmx_unused ed,
t_forcerec *fr,
int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
gmx_membed_t gmx_unused membed,
real gmx_unused cpt_period, real gmx_unused max_hours,
const char gmx_unused *deviceOptions,
int gmx_unused imdport,
unsigned long gmx_unused Flags,
gmx_walltime_accounting_t walltime_accounting)
{
const char *TPI = "Test Particle Insertion";
gmx_localtop_t *top;
gmx_groups_t *groups;
gmx_enerdata_t *enerd;
rvec *f;
real lambda, t, temp, beta, drmax, epot;
double embU, sum_embU, *sum_UgembU, V, V_all, VembU_all;
t_trxstatus *status;
t_trxframe rerun_fr;
gmx_bool bDispCorr, bCharge, bRFExcl, bNotLastFrame, bStateChanged, bNS;
tensor force_vir, shake_vir, vir, pres;
int cg_tp, a_tp0, a_tp1, ngid, gid_tp, nener, e;
rvec *x_mol;
rvec mu_tot, x_init, dx, x_tp;
int nnodes, frame;
gmx_int64_t frame_step_prev, frame_step;
gmx_int64_t nsteps, stepblocksize = 0, step;
gmx_int64_t rnd_count_stride, rnd_count;
gmx_int64_t seed;
double rnd[4];
int i, start, end;
FILE *fp_tpi = NULL;
char *ptr, *dump_pdb, **leg, str[STRLEN], str2[STRLEN];
double dbl, dump_ener;
gmx_bool bCavity;
int nat_cavity = 0, d;
real *mass_cavity = NULL, mass_tot;
int nbin;
double invbinw, *bin, refvolshift, logV, bUlogV;
real dvdl, prescorr, enercorr, dvdlcorr;
gmx_bool bEnergyOutOfBounds;
const char *tpid_leg[2] = {"direct", "reweighted"};
/* Since there is no upper limit to the insertion energies,
* we need to set an upper limit for the distribution output.
*/
real bU_bin_limit = 50;
real bU_logV_bin_limit = bU_bin_limit + 10;
nnodes = cr->nnodes;
top = gmx_mtop_generate_local_top(top_global, inputrec);
groups = &top_global->groups;
bCavity = (inputrec->eI == eiTPIC);
if (bCavity)
{
ptr = getenv("GMX_TPIC_MASSES");
if (ptr == NULL)
{
nat_cavity = 1;
}
else
{
/* Read (multiple) masses from env var GMX_TPIC_MASSES,
* The center of mass of the last atoms is then used for TPIC.
*/
nat_cavity = 0;
while (sscanf(ptr, "%lf%n", &dbl, &i) > 0)
{
srenew(mass_cavity, nat_cavity+1);
mass_cavity[nat_cavity] = dbl;
fprintf(fplog, "mass[%d] = %f\n",
nat_cavity+1, mass_cavity[nat_cavity]);
nat_cavity++;
ptr += i;
}
if (nat_cavity == 0)
{
gmx_fatal(FARGS, "Found %d masses in GMX_TPIC_MASSES", nat_cavity);
}
}
}
/*
init_em(fplog,TPI,inputrec,&lambda,nrnb,mu_tot,
state->box,fr,mdatoms,top,cr,nfile,fnm,NULL,NULL);*/
/* We never need full pbc for TPI */
fr->ePBC = epbcXYZ;
/* Determine the temperature for the Boltzmann weighting */
temp = inputrec->opts.ref_t[0];
if (fplog)
{
for (i = 1; (i < inputrec->opts.ngtc); i++)
{
if (inputrec->opts.ref_t[i] != temp)
{
fprintf(fplog, "\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
fprintf(stderr, "\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
}
}
fprintf(fplog,
"\n The temperature for test particle insertion is %.3f K\n\n",
temp);
}
beta = 1.0/(BOLTZ*temp);
/* Number of insertions per frame */
nsteps = inputrec->nsteps;
/* Use the same neighborlist with more insertions points
* in a sphere of radius drmax around the initial point
*/
/* This should be a proper mdp parameter */
drmax = inputrec->rtpi;
/* An environment variable can be set to dump all configurations
* to pdb with an insertion energy <= this value.
*/
dump_pdb = getenv("GMX_TPI_DUMP");
dump_ener = 0;
if (dump_pdb)
{
sscanf(dump_pdb, "%lf", &dump_ener);
}
atoms2md(top_global, inputrec, 0, NULL, top_global->natoms, mdatoms);
update_mdatoms(mdatoms, inputrec->fepvals->init_lambda);
snew(enerd, 1);
init_enerdata(groups->grps[egcENER].nr, inputrec->fepvals->n_lambda, enerd);
snew(f, top_global->natoms);
/* Print to log file */
walltime_accounting_start(walltime_accounting);
wallcycle_start(wcycle, ewcRUN);
print_start(fplog, cr, walltime_accounting, "Test Particle Insertion");
/* The last charge group is the group to be inserted */
cg_tp = top->cgs.nr - 1;
a_tp0 = top->cgs.index[cg_tp];
a_tp1 = top->cgs.index[cg_tp+1];
if (debug)
{
fprintf(debug, "TPI cg %d, atoms %d-%d\n", cg_tp, a_tp0, a_tp1);
}
if (a_tp1 - a_tp0 > 1 &&
(inputrec->rlist < inputrec->rcoulomb ||
inputrec->rlist < inputrec->rvdw))
{
gmx_fatal(FARGS, "Can not do TPI for multi-atom molecule with a twin-range cut-off");
}
snew(x_mol, a_tp1-a_tp0);
bDispCorr = (inputrec->eDispCorr != edispcNO);
bCharge = FALSE;
for (i = a_tp0; i < a_tp1; i++)
{
/* Copy the coordinates of the molecule to be insterted */
copy_rvec(state->x[i], x_mol[i-a_tp0]);
/* Check if we need to print electrostatic energies */
bCharge |= (mdatoms->chargeA[i] != 0 ||
(mdatoms->chargeB && mdatoms->chargeB[i] != 0));
}
bRFExcl = (bCharge && EEL_RF(fr->eeltype) && fr->eeltype != eelRF_NEC);
calc_cgcm(fplog, cg_tp, cg_tp+1, &(top->cgs), state->x, fr->cg_cm);
if (bCavity)
{
if (norm(fr->cg_cm[cg_tp]) > 0.5*inputrec->rlist && fplog)
{
fprintf(fplog, "WARNING: Your TPI molecule is not centered at 0,0,0\n");
fprintf(stderr, "WARNING: Your TPI molecule is not centered at 0,0,0\n");
}
}
else
{
/* Center the molecule to be inserted at zero */
for (i = 0; i < a_tp1-a_tp0; i++)
{
rvec_dec(x_mol[i], fr->cg_cm[cg_tp]);
}
}
if (fplog)
{
fprintf(fplog, "\nWill insert %d atoms %s partial charges\n",
a_tp1-a_tp0, bCharge ? "with" : "without");
fprintf(fplog, "\nWill insert %d times in each frame of %s\n",
(int)nsteps, opt2fn("-rerun", nfile, fnm));
}
if (!bCavity)
{
if (inputrec->nstlist > 1)
{
if (drmax == 0 && a_tp1-a_tp0 == 1)
{
gmx_fatal(FARGS, "Re-using the neighborlist %d times for insertions of a single atom in a sphere of radius %f does not make sense", inputrec->nstlist, drmax);
}
if (fplog)
{
fprintf(fplog, "Will use the same neighborlist for %d insertions in a sphere of radius %f\n", inputrec->nstlist, drmax);
}
}
}
else
{
if (fplog)
{
fprintf(fplog, "Will insert randomly in a sphere of radius %f around the center of the cavity\n", drmax);
}
}
ngid = groups->grps[egcENER].nr;
gid_tp = GET_CGINFO_GID(fr->cginfo[cg_tp]);
nener = 1 + ngid;
if (bDispCorr)
{
nener += 1;
}
if (bCharge)
{
nener += ngid;
if (bRFExcl)
{
nener += 1;
}
if (EEL_FULL(fr->eeltype))
{
nener += 1;
}
}
snew(sum_UgembU, nener);
/* Copy the random seed set by the user */
seed = inputrec->ld_seed;
/* We use the frame step number as one random counter.
* The second counter use the insertion (step) count. But we
* need multiple random numbers per insertion. This number is
* not fixed, since we generate random locations in a sphere
* by putting locations in a cube and some of these fail.
* A count of 20 is already extremely unlikely, so 10000 is
* a safe margin for random numbers per insertion.
*/
rnd_count_stride = 10000;
if (MASTER(cr))
{
fp_tpi = xvgropen(opt2fn("-tpi", nfile, fnm),
"TPI energies", "Time (ps)",
"(kJ mol\\S-1\\N) / (nm\\S3\\N)", oenv);
xvgr_subtitle(fp_tpi, "f. are averages over one frame", oenv);
snew(leg, 4+nener);
e = 0;
sprintf(str, "-kT log(<Ve\\S-\\betaU\\N>/<V>)");
leg[e++] = strdup(str);
sprintf(str, "f. -kT log<e\\S-\\betaU\\N>");
leg[e++] = strdup(str);
sprintf(str, "f. <e\\S-\\betaU\\N>");
leg[e++] = strdup(str);
sprintf(str, "f. V");
leg[e++] = strdup(str);
sprintf(str, "f. <Ue\\S-\\betaU\\N>");
leg[e++] = strdup(str);
for (i = 0; i < ngid; i++)
{
sprintf(str, "f. <U\\sVdW %s\\Ne\\S-\\betaU\\N>",
*(groups->grpname[groups->grps[egcENER].nm_ind[i]]));
leg[e++] = strdup(str);
}
if (bDispCorr)
{
sprintf(str, "f. <U\\sdisp c\\Ne\\S-\\betaU\\N>");
leg[e++] = strdup(str);
}
if (bCharge)
{
for (i = 0; i < ngid; i++)
{
sprintf(str, "f. <U\\sCoul %s\\Ne\\S-\\betaU\\N>",
*(groups->grpname[groups->grps[egcENER].nm_ind[i]]));
leg[e++] = strdup(str);
}
if (bRFExcl)
{
sprintf(str, "f. <U\\sRF excl\\Ne\\S-\\betaU\\N>");
leg[e++] = strdup(str);
}
if (EEL_FULL(fr->eeltype))
{
sprintf(str, "f. <U\\sCoul recip\\Ne\\S-\\betaU\\N>");
leg[e++] = strdup(str);
}
}
xvgr_legend(fp_tpi, 4+nener, (const char**)leg, oenv);
for (i = 0; i < 4+nener; i++)
{
sfree(leg[i]);
}
sfree(leg);
}
clear_rvec(x_init);
V_all = 0;
VembU_all = 0;
invbinw = 10;
nbin = 10;
snew(bin, nbin);
/* Avoid frame step numbers <= -1 */
frame_step_prev = -1;
bNotLastFrame = read_first_frame(oenv, &status, opt2fn("-rerun", nfile, fnm),
&rerun_fr, TRX_NEED_X);
frame = 0;
if (rerun_fr.natoms - (bCavity ? nat_cavity : 0) !=
mdatoms->nr - (a_tp1 - a_tp0))
{
gmx_fatal(FARGS, "Number of atoms in trajectory (%d)%s "
"is not equal the number in the run input file (%d) "
"minus the number of atoms to insert (%d)\n",
rerun_fr.natoms, bCavity ? " minus one" : "",
mdatoms->nr, a_tp1-a_tp0);
}
refvolshift = log(det(rerun_fr.box));
switch (inputrec->eI)
{
case eiTPI:
stepblocksize = inputrec->nstlist;
break;
case eiTPIC:
stepblocksize = 1;
break;
default:
gmx_fatal(FARGS, "Unknown integrator %s", ei_names[inputrec->eI]);
}
#ifdef GMX_SIMD
/* Make sure we don't detect SIMD overflow generated before this point */
gmx_simd_check_and_reset_overflow();
#endif
while (bNotLastFrame)
{
frame_step = rerun_fr.step;
if (frame_step <= frame_step_prev)
{
/* We don't have step number in the trajectory file,
* or we have constant or decreasing step numbers.
* Ensure we have increasing step numbers, since we use
* the step numbers as a counter for random numbers.
*/
frame_step = frame_step_prev + 1;
}
frame_step_prev = frame_step;
lambda = rerun_fr.lambda;
t = rerun_fr.time;
sum_embU = 0;
for (e = 0; e < nener; e++)
{
sum_UgembU[e] = 0;
}
/* Copy the coordinates from the input trajectory */
for (i = 0; i < rerun_fr.natoms; i++)
{
copy_rvec(rerun_fr.x[i], state->x[i]);
}
copy_mat(rerun_fr.box, state->box);
V = det(state->box);
logV = log(V);
bStateChanged = TRUE;
bNS = TRUE;
step = cr->nodeid*stepblocksize;
while (step < nsteps)
{
/* Initialize the second counter for random numbers using
* the insertion step index. This ensures that we get
* the same random numbers independently of how many
* MPI ranks we use. Also for the same seed, we get
* the same initial random sequence for different nsteps.
*/
rnd_count = step*rnd_count_stride;
if (!bCavity)
{
/* Random insertion in the whole volume */
bNS = (step % inputrec->nstlist == 0);
if (bNS)
{
/* Generate a random position in the box */
gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd);
gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd+2);
for (d = 0; d < DIM; d++)
{
x_init[d] = rnd[d]*state->box[d][d];
}
}
if (inputrec->nstlist == 1)
{
copy_rvec(x_init, x_tp);
}
else
{
/* Generate coordinates within |dx|=drmax of x_init */
do
{
gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd);
gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd+2);
for (d = 0; d < DIM; d++)
{
dx[d] = (2*rnd[d] - 1)*drmax;
}
}
while (norm2(dx) > drmax*drmax);
rvec_add(x_init, dx, x_tp);
}
}
else
{
/* Random insertion around a cavity location
* given by the last coordinate of the trajectory.
*/
if (step == 0)
{
if (nat_cavity == 1)
{
/* Copy the location of the cavity */
copy_rvec(rerun_fr.x[rerun_fr.natoms-1], x_init);
}
else
{
/* Determine the center of mass of the last molecule */
clear_rvec(x_init);
mass_tot = 0;
for (i = 0; i < nat_cavity; i++)
{
for (d = 0; d < DIM; d++)
{
x_init[d] +=
mass_cavity[i]*rerun_fr.x[rerun_fr.natoms-nat_cavity+i][d];
}
mass_tot += mass_cavity[i];
}
for (d = 0; d < DIM; d++)
{
x_init[d] /= mass_tot;
}
}
}
/* Generate coordinates within |dx|=drmax of x_init */
do
{
gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd);
gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd+2);
for (d = 0; d < DIM; d++)
{
dx[d] = (2*rnd[d] - 1)*drmax;
}
}
while (norm2(dx) > drmax*drmax);
rvec_add(x_init, dx, x_tp);
}
if (a_tp1 - a_tp0 == 1)
{
/* Insert a single atom, just copy the insertion location */
copy_rvec(x_tp, state->x[a_tp0]);
}
else
{
/* Copy the coordinates from the top file */
for (i = a_tp0; i < a_tp1; i++)
{
copy_rvec(x_mol[i-a_tp0], state->x[i]);
}
/* Rotate the molecule randomly */
gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd);
gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd+2);
rotate_conf(a_tp1-a_tp0, state->x+a_tp0, NULL,
2*M_PI*rnd[0],
2*M_PI*rnd[1],
2*M_PI*rnd[2]);
/* Shift to the insertion location */
for (i = a_tp0; i < a_tp1; i++)
{
rvec_inc(state->x[i], x_tp);
}
}
/* Clear some matrix variables */
clear_mat(force_vir);
clear_mat(shake_vir);
clear_mat(vir);
clear_mat(pres);
/* Set the charge group center of mass of the test particle */
copy_rvec(x_init, fr->cg_cm[top->cgs.nr-1]);
/* Calc energy (no forces) on new positions.
* Since we only need the intermolecular energy
* and the RF exclusion terms of the inserted molecule occur
* within a single charge group we can pass NULL for the graph.
* This also avoids shifts that would move charge groups
* out of the box.
*
* Some checks above ensure than we can not have
* twin-range interactions together with nstlist > 1,
* therefore we do not need to remember the LR energies.
*/
/* Make do_force do a single node force calculation */
cr->nnodes = 1;
do_force(fplog, cr, inputrec,
step, nrnb, wcycle, top, &top_global->groups,
state->box, state->x, &state->hist,
f, force_vir, mdatoms, enerd, fcd,
state->lambda,
NULL, fr, NULL, mu_tot, t, NULL, NULL, FALSE,
GMX_FORCE_NONBONDED | GMX_FORCE_ENERGY |
(bNS ? GMX_FORCE_DYNAMICBOX | GMX_FORCE_NS | GMX_FORCE_DO_LR : 0) |
(bStateChanged ? GMX_FORCE_STATECHANGED : 0));
cr->nnodes = nnodes;
bStateChanged = FALSE;
bNS = FALSE;
/* Calculate long range corrections to pressure and energy */
calc_dispcorr(fplog, inputrec, fr, step, top_global->natoms, state->box,
lambda, pres, vir, &prescorr, &enercorr, &dvdlcorr);
/* figure out how to rearrange the next 4 lines MRS 8/4/2009 */
enerd->term[F_DISPCORR] = enercorr;
enerd->term[F_EPOT] += enercorr;
enerd->term[F_PRES] += prescorr;
enerd->term[F_DVDL_VDW] += dvdlcorr;
epot = enerd->term[F_EPOT];
bEnergyOutOfBounds = FALSE;
#ifdef GMX_SIMD_X86_SSE2_OR_HIGHER
/* With SSE the energy can overflow, check for this */
if (gmx_mm_check_and_reset_overflow())
{
if (debug)
{
fprintf(debug, "Found an SSE overflow, assuming the energy is out of bounds\n");
}
bEnergyOutOfBounds = TRUE;
}
#endif
/* If the compiler doesn't optimize this check away
* we catch the NAN energies.
* The epot>GMX_REAL_MAX check catches inf values,
* which should nicely result in embU=0 through the exp below,
* but it does not hurt to check anyhow.
*/
/* Non-bonded Interaction usually diverge at r=0.
* With tabulated interaction functions the first few entries
* should be capped in a consistent fashion between
* repulsion, dispersion and Coulomb to avoid accidental
* negative values in the total energy.
* The table generation code in tables.c does this.
* With user tbales the user should take care of this.
*/
if (epot != epot || epot > GMX_REAL_MAX)
{
bEnergyOutOfBounds = TRUE;
}
if (bEnergyOutOfBounds)
{
if (debug)
{
fprintf(debug, "\n time %.3f, step %d: non-finite energy %f, using exp(-bU)=0\n", t, (int)step, epot);
}
embU = 0;
}
else
{
embU = exp(-beta*epot);
sum_embU += embU;
/* Determine the weighted energy contributions of each energy group */
e = 0;
sum_UgembU[e++] += epot*embU;
if (fr->bBHAM)
{
for (i = 0; i < ngid; i++)
{
sum_UgembU[e++] +=
(enerd->grpp.ener[egBHAMSR][GID(i, gid_tp, ngid)] +
enerd->grpp.ener[egBHAMLR][GID(i, gid_tp, ngid)])*embU;
}
}
else
{
for (i = 0; i < ngid; i++)
{
sum_UgembU[e++] +=
(enerd->grpp.ener[egLJSR][GID(i, gid_tp, ngid)] +
enerd->grpp.ener[egLJLR][GID(i, gid_tp, ngid)])*embU;
}
}
if (bDispCorr)
{
sum_UgembU[e++] += enerd->term[F_DISPCORR]*embU;
}
if (bCharge)
{
for (i = 0; i < ngid; i++)
{
sum_UgembU[e++] +=
(enerd->grpp.ener[egCOULSR][GID(i, gid_tp, ngid)] +
enerd->grpp.ener[egCOULLR][GID(i, gid_tp, ngid)])*embU;
}
if (bRFExcl)
{
sum_UgembU[e++] += enerd->term[F_RF_EXCL]*embU;
}
if (EEL_FULL(fr->eeltype))
{
sum_UgembU[e++] += enerd->term[F_COUL_RECIP]*embU;
}
}
}
if (embU == 0 || beta*epot > bU_bin_limit)
{
bin[0]++;
}
else
{
i = (int)((bU_logV_bin_limit
- (beta*epot - logV + refvolshift))*invbinw
+ 0.5);
if (i < 0)
{
i = 0;
}
if (i >= nbin)
{
realloc_bins(&bin, &nbin, i+10);
}
bin[i]++;
}
if (debug)
{
fprintf(debug, "TPI %7d %12.5e %12.5f %12.5f %12.5f\n",
(int)step, epot, x_tp[XX], x_tp[YY], x_tp[ZZ]);
}
if (dump_pdb && epot <= dump_ener)
{
sprintf(str, "t%g_step%d.pdb", t, (int)step);
sprintf(str2, "t: %f step %d ener: %f", t, (int)step, epot);
write_sto_conf_mtop(str, str2, top_global, state->x, state->v,
inputrec->ePBC, state->box);
}
step++;
if ((step/stepblocksize) % cr->nnodes != cr->nodeid)
{
/* Skip all steps assigned to the other MPI ranks */
step += (cr->nnodes - 1)*stepblocksize;
}
}
if (PAR(cr))
{
/* When running in parallel sum the energies over the processes */
gmx_sumd(1, &sum_embU, cr);
gmx_sumd(nener, sum_UgembU, cr);
}
frame++;
V_all += V;
VembU_all += V*sum_embU/nsteps;
if (fp_tpi)
{
if (bVerbose || frame%10 == 0 || frame < 10)
{
fprintf(stderr, "mu %10.3e <mu> %10.3e\n",
-log(sum_embU/nsteps)/beta, -log(VembU_all/V_all)/beta);
}
fprintf(fp_tpi, "%10.3f %12.5e %12.5e %12.5e %12.5e",
t,
VembU_all == 0 ? 20/beta : -log(VembU_all/V_all)/beta,
sum_embU == 0 ? 20/beta : -log(sum_embU/nsteps)/beta,
sum_embU/nsteps, V);
for (e = 0; e < nener; e++)
{
fprintf(fp_tpi, " %12.5e", sum_UgembU[e]/nsteps);
}
fprintf(fp_tpi, "\n");
fflush(fp_tpi);
}
bNotLastFrame = read_next_frame(oenv, status, &rerun_fr);
} /* End of the loop */
walltime_accounting_end(walltime_accounting);
close_trj(status);
if (fp_tpi != NULL)
{
gmx_fio_fclose(fp_tpi);
}
if (fplog != NULL)
{
fprintf(fplog, "\n");
fprintf(fplog, " <V> = %12.5e nm^3\n", V_all/frame);
fprintf(fplog, " <mu> = %12.5e kJ/mol\n", -log(VembU_all/V_all)/beta);
}
/* Write the Boltzmann factor histogram */
if (PAR(cr))
{
/* When running in parallel sum the bins over the processes */
i = nbin;
global_max(cr, &i);
realloc_bins(&bin, &nbin, i);
gmx_sumd(nbin, bin, cr);
}
if (MASTER(cr))
{
fp_tpi = xvgropen(opt2fn("-tpid", nfile, fnm),
"TPI energy distribution",
"\\betaU - log(V/<V>)", "count", oenv);
sprintf(str, "number \\betaU > %g: %9.3e", bU_bin_limit, bin[0]);
xvgr_subtitle(fp_tpi, str, oenv);
xvgr_legend(fp_tpi, 2, (const char **)tpid_leg, oenv);
for (i = nbin-1; i > 0; i--)
{
bUlogV = -i/invbinw + bU_logV_bin_limit - refvolshift + log(V_all/frame);
fprintf(fp_tpi, "%6.2f %10d %12.5e\n",
bUlogV,
(int)(bin[i]+0.5),
bin[i]*exp(-bUlogV)*V_all/VembU_all);
}
gmx_fio_fclose(fp_tpi);
}
sfree(bin);
sfree(sum_UgembU);
walltime_accounting_set_nsteps_done(walltime_accounting, frame*inputrec->nsteps);
return 0;
}
void virial(FILE *fp,gmx_bool bFull,int nmol,rvec x[],matrix box,real rcut,
gmx_bool bYaw,real q[],gmx_bool bLJ)
{
int i,j,im,jm,natmol,ik,jk,m,ninter;
rvec dx,f,ftot,dvir,vir,pres,xcmi,xcmj,*force;
real dx6,dx2,dx1,fscal,c6,c12,vcoul,v12,v6,vctot,v12tot,v6tot;
t_pbc pbc;
set_pbc(&pbc,box);
fprintf(fp,"%3s - %3s: %6s %6s %6s %6s %8s %8s %8s\n",
"ai","aj","dx","dy","dz","|d|","virx","viry","virz");
clear_rvec(ftot);
clear_rvec(vir);
ninter = 0;
vctot = 0;
v12tot = 0;
v6tot = 0;
natmol = bYaw ? 5 : 3;
snew(force,nmol*natmol);
for(i=0; (i<nmol); i++) {
im = natmol*i;
/* Center of geometry */
clear_rvec(xcmi);
for(ik=0; (ik<natmol); ik++)
rvec_inc(xcmi,x[im+ik]);
for(m=0; (m<DIM); m++)
xcmi[m] /= natmol;
for(j=i+1; (j<nmol); j++) {
jm = natmol*j;
/* Center of geometry */
clear_rvec(xcmj);
for(jk=0; (jk<natmol); jk++)
rvec_inc(xcmj,x[jm+jk]);
for(m=0; (m<DIM); m++)
xcmj[m] /= natmol;
/* First check COM-COM distance */
pbc_dx(&pbc,xcmi,xcmj,dx);
if (norm(dx) < rcut) {
ninter++;
/* Neirest neighbour molecules! */
clear_rvec(dvir);
for(ik=0; (ik<natmol); ik++) {
for(jk=0; (jk<natmol); jk++) {
pbc_dx(&pbc,x[im+ik],x[jm+jk],dx);
dx2 = iprod(dx,dx);
dx1 = sqrt(dx2);
vcoul = q[ik]*q[jk]*ONE_4PI_EPS0/dx1;
vctot += vcoul;
if (bLJ) {
if (bYaw) {
c6 = yaw_lj[ik][2*jk];
c12 = yaw_lj[ik][2*jk+1];
}
else {
c6 = spc_lj[ik][2*jk];
c12 = spc_lj[ik][2*jk+1];
}
dx6 = dx2*dx2*dx2;
v6 = c6/dx6;
v12 = c12/(dx6*dx6);
v6tot -= v6;
v12tot+= v12;
fscal = (vcoul+12*v12-6*v6)/dx2;
}
else
fscal = vcoul/dx2;
for(m=0; (m<DIM); m++) {
f[m] = dx[m]*fscal;
dvir[m] -= 0.5*dx[m]*f[m];
}
rvec_inc(force[ik+im],f);
rvec_dec(force[jk+jm],f);
/*if (bFull)
fprintf(fp,"%3s%4d-%3s%4d: %6.3f %6.3f %6.3f %6.3f"
" %8.3f %8.3f %8.3f\n",
watname[ik],im+ik,watname[jk],jm+jk,
dx[XX],dx[YY],dx[ZZ],norm(dx),
dvir[XX],dvir[YY],dvir[ZZ]);*/
}
}
if (bFull)
fprintf(fp,"%3s%4d-%3s%4d: "
" %8.3f %8.3f %8.3f\n",
"SOL",i,"SOL",j,dvir[XX],dvir[YY],dvir[ZZ]);
rvec_inc(vir,dvir);
}
}
}
fprintf(fp,"There were %d interactions between the %d molecules (%.2f %%)\n",
ninter,nmol,(real)ninter/(0.5*nmol*(nmol-1)));
fprintf(fp,"Vcoul: %10.4e V12: %10.4e V6: %10.4e Vtot: %10.4e (kJ/mol)\n",
vctot/nmol,v12tot/nmol,v6tot/nmol,(vctot+v12tot+v6tot)/nmol);
pr_rvec(fp,0,"vir ",vir,DIM,TRUE);
for(m=0; (m<DIM); m++)
pres[m] = -2*PRESFAC/(det(box))*vir[m];
pr_rvec(fp,0,"pres",pres,DIM,TRUE);
pr_rvecs(fp,0,"force",force,natmol*nmol);
sfree(force);
}