本文整理汇总了C++中rvec_dec函数的典型用法代码示例。如果您正苦于以下问题：C++ rvec_dec函数的具体用法？C++ rvec_dec怎么用？C++ rvec_dec使用的例子？那么恭喜您, 这里精选的函数代码示例或许可以为您提供帮助。
在下文中一共展示了rvec_dec函数的15个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的C++代码示例。
示例1: reset_x_ndim
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);
}示例2: reset_x_ndim
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);
}
}
}示例3: calc_axes
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]);
}
}示例4: prep_data
/* 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]);
}
}
}示例5: center_coords
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);
}
}示例6: do_stopcm_grp
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);
}
}
}
}示例7: my_sub_xcm
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);
}
}示例8: sub_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;
}示例9: center_molecule
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);
}
}示例10: correct_box_elem
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;
}示例11: copy_mat
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];
}
}示例12: print_constraint
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 */
}示例13: prep_data
/* 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]);
}
}
}
}示例14: correct_t0_pbc
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]);
}示例15: calc_com2
/* 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;
}