本文整理汇总了C++中pbc_dx函数的典型用法代码示例。如果您正苦于以下问题：C++ pbc_dx函数的具体用法？C++ pbc_dx怎么用？C++ pbc_dx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pbc_dx函数的20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，您的评价将有助于我们的系统推荐出更棒的C++代码示例。
示例1: allPairsDistOk
/* This is a (maybe) slow workaround to avoid the neighbor searching in addconf.c, which
* leaks memory (May 2012). The function could be deleted as soon as the momory leaks
* in addconf.c are fixed.
* However, when inserting a small molecule in a system containing not too many atoms,
* allPairsDistOk is probably even faster than addconf.c
*/
static gmx_bool
allPairsDistOk(t_atoms *atoms, rvec *x, real *r,
int ePBC, matrix box,
t_atoms *atoms_insrt, rvec *x_n, real *r_insrt)
{
int i, j;
rvec dx;
real n2, r2;
t_pbc pbc;
set_pbc(&pbc, ePBC, box);
for (i = 0; i < atoms->nr; i++)
{
for (j = 0; j < atoms_insrt->nr; j++)
{
pbc_dx(&pbc, x[i], x_n[j], dx);
n2 = norm2(dx);
r2 = sqr(r[i]+r_insrt[j]);
if (n2 < r2)
{
return FALSE;
}
}
}
return TRUE;
}
开发者ID:alwanderer，项目名称:gromacs，代码行数:32，代码来源:gmx_genbox.cpp
示例2: calc_dist_tot
static void calc_dist_tot(int nind, atom_id index[], rvec x[],
int ePBC, matrix box,
real **d, real **dtot, real **dtot2,
gmx_bool bNMR, real **dtot1_3, real **dtot1_6)
{
int i, j;
real *xi;
real temp, temp2, temp1_3;
rvec dx;
t_pbc pbc;
set_pbc(&pbc, ePBC, box);
for (i = 0; (i < nind-1); i++)
{
xi = x[index[i]];
for (j = i+1; (j < nind); j++)
{
pbc_dx(&pbc, xi, x[index[j]], dx);
temp2 = norm2(dx);
temp = std::sqrt(temp2);
d[i][j] = temp;
dtot[i][j] += temp;
dtot2[i][j] += temp2;
if (bNMR)
{
temp1_3 = 1.0/(temp*temp2);
dtot1_3[i][j] += temp1_3;
dtot1_6[i][j] += temp1_3*temp1_3;
}
}
}
}
开发者ID:mpharrigan，项目名称:gromacs，代码行数:32，代码来源:gmx_rmsdist.cpp
示例3: pbc_dx
void
Distance::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
TrajectoryAnalysisModuleData *pdata)
{
AnalysisDataHandle dh = pdata->dataHandle(data_);
const Selection &sel1 = pdata->parallelSelection(sel_[0]);
const Selection &sel2 = pdata->parallelSelection(sel_[1]);
rvec dx;
real r;
const SelectionPosition &p1 = sel1.position(0);
const SelectionPosition &p2 = sel2.position(0);
if (pbc != NULL)
{
pbc_dx(pbc, p1.x(), p2.x(), dx);
}
else
{
rvec_sub(p1.x(), p2.x(), dx);
}
r = norm(dx);
dh.startFrame(frnr, fr.time);
dh.setPoint(0, r);
dh.setPoints(1, 3, dx);
dh.finishFrame();
}
开发者ID:hasagar，项目名称:gromacs，代码行数:26，代码来源:distance.cpp
示例4: mk_bonds
void mk_bonds(int nnm, t_nm2type nmt[],
t_atoms *atoms, rvec x[], t_params *bond, int nbond[],
gmx_bool bPBC, matrix box)
{
t_param b;
int i, j;
t_pbc pbc;
rvec dx;
real dx2;
for (i = 0; (i < MAXATOMLIST); i++)
{
b.a[i] = -1;
}
for (i = 0; (i < MAXFORCEPARAM); i++)
{
b.c[i] = 0.0;
}
if (bPBC)
{
set_pbc(&pbc, -1, box);
}
for (i = 0; (i < atoms->nr); i++)
{
if ((i % 10) == 0)
{
fprintf(stderr, "\ratom %d", i);
}
for (j = i+1; (j < atoms->nr); j++)
{
if (bPBC)
{
pbc_dx(&pbc, x[i], x[j], dx);
}
else
{
rvec_sub(x[i], x[j], dx);
}
dx2 = iprod(dx, dx);
if (is_bond(nnm, nmt, *atoms->atomname[i], *atoms->atomname[j],
sqrt(dx2)))
{
b.AI = i;
b.AJ = j;
b.C0 = sqrt(dx2);
add_param_to_list (bond, &b);
nbond[i]++;
nbond[j]++;
if (debug)
{
fprintf(debug, "Bonding atoms %s-%d and %s-%d\n",
*atoms->atomname[i], i+1, *atoms->atomname[j], j+1);
}
}
}
}
fprintf(stderr, "\ratom %d\n", i);
}
开发者ID:exianshine，项目名称:gromacs，代码行数:60，代码来源:g_x2top.c
示例5: set_pbc
static t_bbb *mk_bonds(int natoms,rvec x[],real odist,
gmx_bool bPBC,matrix box)
{
real od2 = odist*odist+1e-5;
t_pbc pbc;
t_bbb *bbb;
int i,j;
rvec dx;
if (bPBC)
set_pbc(&pbc,box);
snew(bbb,natoms);
for(i=0; (i<natoms); i++) {
for(j=i+1; (j<natoms); j++) {
if (bPBC)
pbc_dx(&pbc,x[i],x[j],dx);
else
rvec_sub(x[i],x[j],dx);
if (iprod(dx,dx) <= od2) {
bbb[i].aa[bbb[i].n++] = j;
bbb[j].aa[bbb[j].n++] = i;
}
}
}
if (debug)
#define PRB(nn) (bbb[(i)].n >= (nn)) ? bbb[i].aa[nn-1] : -1
for(i=0; (i<natoms); i++)
fprintf(debug,"bonds from %3d: %d %d %d %d\n",
i,PRB(1),PRB(2),PRB(3),PRB(4));
#undef PRB
return bbb;
}
开发者ID:daniellandau，项目名称:gromacs，代码行数:32，代码来源:mkice.c
示例6: dist2
static real dist2(t_pbc *pbc,rvec x,rvec y)
{
rvec dx;
pbc_dx(pbc,x,y,dx);
return norm2(dx);
}
开发者ID:TTarenzi，项目名称:MMCG-HAdResS，代码行数:8，代码来源:gbutil.c
示例7: calc_com_pbc
static void calc_com_pbc(int nrefat, t_topology *top, rvec x[], t_pbc *pbc,
atom_id index[], rvec xref, int ePBC)
{
const real tol = 1e-4;
gmx_bool bChanged;
int m, j, ai, iter;
real mass, mtot;
rvec dx, xtest;
/* First simple calculation */
clear_rvec(xref);
mtot = 0;
for (m = 0; (m < nrefat); m++)
{
ai = index[m];
mass = top->atoms.atom[ai].m;
for (j = 0; (j < DIM); j++)
{
xref[j] += mass*x[ai][j];
}
mtot += mass;
}
svmul(1/mtot, xref, xref);
/* Now check if any atom is more than half the box from the COM */
if (ePBC != epbcNONE)
{
iter = 0;
do
{
bChanged = FALSE;
for (m = 0; (m < nrefat); m++)
{
ai = index[m];
mass = top->atoms.atom[ai].m/mtot;
pbc_dx(pbc, x[ai], xref, dx);
rvec_add(xref, dx, xtest);
for (j = 0; (j < DIM); j++)
{
if (std::abs(xtest[j]-x[ai][j]) > tol)
{
/* Here we have used the wrong image for contributing to the COM */
xref[j] += mass*(xtest[j]-x[ai][j]);
x[ai][j] = xtest[j];
bChanged = TRUE;
}
}
}
if (bChanged)
{
printf("COM: %8.3f %8.3f %8.3f iter = %d\n", xref[XX], xref[YY], xref[ZZ], iter);
}
iter++;
}
while (bChanged);
}
}
开发者ID:carryer123，项目名称:gromacs，代码行数:56，代码来源:gmx_spol.cpp
示例8: chk_bonds
static void chk_bonds(t_idef *idef, int ePBC, rvec *x, matrix box, real tol)
{
int ftype, i, k, ai, aj, type;
real b0, blen, deviation, devtot;
t_pbc pbc;
rvec dx;
devtot = 0;
set_pbc(&pbc, ePBC, box);
for (ftype = 0; (ftype < F_NRE); ftype++)
{
if ((interaction_function[ftype].flags & IF_CHEMBOND) == IF_CHEMBOND)
{
for (k = 0; (k < idef->il[ftype].nr); )
{
type = idef->il[ftype].iatoms[k++];
ai = idef->il[ftype].iatoms[k++];
aj = idef->il[ftype].iatoms[k++];
b0 = 0;
switch (ftype)
{
case F_BONDS:
b0 = idef->iparams[type].harmonic.rA;
break;
case F_G96BONDS:
b0 = sqrt(idef->iparams[type].harmonic.rA);
break;
case F_MORSE:
b0 = idef->iparams[type].morse.b0A;
break;
case F_CUBICBONDS:
b0 = idef->iparams[type].cubic.b0;
break;
case F_CONSTR:
b0 = idef->iparams[type].constr.dA;
break;
default:
break;
}
if (b0 != 0)
{
pbc_dx(&pbc, x[ai], x[aj], dx);
blen = norm(dx);
deviation = sqr(blen-b0);
if (sqrt(deviation/sqr(b0) > tol))
{
fprintf(stderr, "Distance between atoms %d and %d is %.3f, should be %.3f\n", ai+1, aj+1, blen, b0);
}
}
}
}
}
}
开发者ID:dkarkoulis，项目名称:gromacs，代码行数:53，代码来源:check.c
示例9: calc_vec
//! Helper method to calculate a vector from two or three positions.
static void
calc_vec(int natoms, rvec x[], t_pbc *pbc, rvec xout, rvec cout)
{
switch (natoms)
{
case 2:
if (pbc)
{
pbc_dx(pbc, x[1], x[0], xout);
}
else
{
rvec_sub(x[1], x[0], xout);
}
svmul(0.5, xout, cout);
rvec_add(x[0], cout, cout);
break;
case 3:
{
rvec v1, v2;
if (pbc)
{
pbc_dx(pbc, x[1], x[0], v1);
pbc_dx(pbc, x[2], x[0], v2);
}
else
{
rvec_sub(x[1], x[0], v1);
rvec_sub(x[2], x[0], v2);
}
cprod(v1, v2, xout);
rvec_add(x[0], x[1], cout);
rvec_add(cout, x[2], cout);
svmul(1.0/3.0, cout, cout);
break;
}
default:
GMX_RELEASE_ASSERT(false, "Incorrectly initialized number of atoms");
}
}
开发者ID:smendozabarrera，项目名称:gromacs，代码行数:41，代码来源:angle.cpp
示例10: gmx_calc_com_pbc
/*!
* \param[in] top Topology structure with masses.
* \param[in] x Position vectors of all atoms.
* \param[in] pbc Periodic boundary conditions structure.
* \param[in] nrefat Number of atoms in the index.
* \param[in] index Indices of atoms.
* \param[out] xout COM position for the indexed atoms.
*
* Works as gmx_calc_com(), but takes into account periodic boundary
* conditions: If any atom is more than half the box from the COM,
* it is wrapped around and a new COM is calculated. This is repeated
* until no atoms violate the condition.
*
* Modified from src/tools/gmx_sorient.c in Gromacs distribution.
*/
void
gmx_calc_com_pbc(const gmx_mtop_t *top, rvec x[], const t_pbc *pbc,
int nrefat, const int index[], rvec xout)
{
GMX_RELEASE_ASSERT(gmx_mtop_has_masses(top),
"No masses available while mass weighting was requested");
/* First simple calculation */
clear_rvec(xout);
real mtot = 0;
int molb = 0;
for (int m = 0; m < nrefat; ++m)
{
const int ai = index[m];
const real mass = mtopGetAtomMass(top, ai, &molb);
for (int j = 0; j < DIM; ++j)
{
xout[j] += mass * x[ai][j];
}
mtot += mass;
}
svmul(1.0/mtot, xout, xout);
/* Now check if any atom is more than half the box from the COM */
if (pbc)
{
const real tol = 1e-4;
bool bChanged;
do
{
bChanged = false;
molb = 0;
for (int m = 0; m < nrefat; ++m)
{
rvec dx, xtest;
const int ai = index[m];
const real mass = mtopGetAtomMass(top, ai, &molb) / mtot;
pbc_dx(pbc, x[ai], xout, dx);
rvec_add(xout, dx, xtest);
for (int j = 0; j < DIM; ++j)
{
if (fabs(xtest[j] - x[ai][j]) > tol)
{
/* Here we have used the wrong image for contributing to the COM */
xout[j] += mass * (xtest[j] - x[ai][j]);
x[ai][j] = xtest[j];
bChanged = true;
}
}
}
}
while (bChanged);
}
}
开发者ID:MrTheodor，项目名称:gromacs，代码行数:67，代码来源:centerofmass.cpp
示例11: pbc_dx
// **************** PERIODIC BOUNDARY CONDITIONS ****************
// Get the PBC-aware distance vector between two positions
cvm::rvector colvarproxy_gromacs::position_distance (cvm::atom_pos const &pos1,
cvm::atom_pos const &pos2) {
rvec r1, r2, dr;
r1[0] = pos1.x;
r1[1] = pos1.y;
r1[2] = pos1.z;
r2[0] = pos2.x;
r2[1] = pos2.y;
r2[2] = pos2.z;
pbc_dx(&gmx_pbc, r1, r2, dr);
return cvm::atom_pos( dr[0], dr[1], dr[2] );
}
开发者ID:alejob，项目名称:colvars，代码行数:15，代码来源:colvarproxy_gromacs.cpp
示例12: calc_vec
static void
calc_vec(int natoms, rvec x[], t_pbc *pbc, rvec xout, rvec cout)
{
switch (natoms)
{
case 2:
if (pbc)
{
pbc_dx(pbc, x[1], x[0], xout);
}
else
{
rvec_sub(x[1], x[0], xout);
}
svmul(0.5, xout, cout);
rvec_add(x[0], cout, cout);
break;
case 3: {
rvec v1, v2;
if (pbc)
{
pbc_dx(pbc, x[1], x[0], v1);
pbc_dx(pbc, x[2], x[0], v2);
}
else
{
rvec_sub(x[1], x[0], v1);
rvec_sub(x[2], x[0], v2);
}
cprod(v1, v2, xout);
rvec_add(x[0], x[1], cout);
rvec_add(cout, x[2], cout);
svmul(1.0/3.0, cout, cout);
break;
}
}
}
开发者ID:alexholehouse，项目名称:gromacs，代码行数:37，代码来源:angle.cpp
示例13: calc_mj
static void calc_mj(t_topology top, int ePBC, matrix box, gmx_bool bNoJump, int isize, int index0[], \
rvec fr[], rvec mj, real mass2[], real qmol[])
{
int i, j, k, l;
rvec tmp;
rvec center;
rvec mt1, mt2;
t_pbc pbc;
calc_box_center(ecenterRECT, box, center);
if (!bNoJump)
{
set_pbc(&pbc, ePBC, box);
}
clear_rvec(tmp);
for (i = 0; i < isize; i++)
{
clear_rvec(mt1);
clear_rvec(mt2);
k = top.mols.index[index0[i]];
l = top.mols.index[index0[i+1]];
for (j = k; j < l; j++)
{
svmul(mass2[j], fr[j], tmp);
rvec_inc(mt1, tmp);
}
if (bNoJump)
{
svmul(qmol[k], mt1, mt1);
}
else
{
pbc_dx(&pbc, mt1, center, mt2);
svmul(qmol[k], mt2, mt1);
}
rvec_inc(mj, mt1);
}
}
开发者ID:pjohansson，项目名称:gromacs，代码行数:48，代码来源:gmx_current.cpp
示例14: calc_dist
static real calc_dist(t_pbc *pbc,rvec x[],t_block *cgs,int icg,int jcg)
{
int i,j;
rvec dx;
real d2,mindist2=1000;
for(i=cgs->index[icg]; (i<cgs->index[icg+1]); i++) {
for(j=cgs->index[jcg]; (j<cgs->index[jcg+1]); j++) {
pbc_dx(pbc,x[i],x[j],dx);
d2 = norm2(dx);
if (d2 < mindist2)
mindist2 = d2;
}
}
return sqrt(mindist2);
}
开发者ID:BradleyDickson，项目名称:ABPenabledGROMACS，代码行数:16，代码来源:gmx_saltbr.c
示例15: calc_mat
static void calc_mat(int nres, int natoms, int rndx[],
rvec x[], atom_id *index,
real trunc, real **mdmat, int **nmat, int ePBC, matrix box)
{
int i, j, resi, resj;
real trunc2, r, r2;
t_pbc pbc;
rvec ddx;
set_pbc(&pbc, ePBC, box);
trunc2 = sqr(trunc);
for (resi = 0; (resi < nres); resi++)
{
for (resj = 0; (resj < nres); resj++)
{
mdmat[resi][resj] = FARAWAY;
}
}
for (i = 0; (i < natoms); i++)
{
resi = rndx[i];
for (j = i+1; (j < natoms); j++)
{
resj = rndx[j];
pbc_dx(&pbc, x[index[i]], x[index[j]], ddx);
r2 = norm2(ddx);
if (r2 < trunc2)
{
nmat[resi][j]++;
nmat[resj][i]++;
}
mdmat[resi][resj] = min(r2, mdmat[resi][resj]);
}
}
for (resi = 0; (resi < nres); resi++)
{
mdmat[resi][resi] = 0;
for (resj = resi+1; (resj < nres); resj++)
{
r = sqrt(mdmat[resi][resj]);
mdmat[resi][resj] = r;
mdmat[resj][resi] = r;
}
}
}
开发者ID:yhalcyon，项目名称:Gromacs，代码行数:46，代码来源:gmx_mdmat.c
示例16: put_atoms_in_compact_unitcell
const char *
put_atoms_in_compact_unitcell(int ePBC,int ecenter,matrix box,
int natoms,rvec x[])
{
t_pbc pbc;
rvec box_center,dx;
int i;
set_pbc(&pbc,ePBC,box);
calc_box_center(ecenter,box,box_center);
for(i=0; i<natoms; i++) {
pbc_dx(&pbc,x[i],box_center,dx);
rvec_add(box_center,dx,x[i]);
}
return pbc.bLimitDistance ?
"WARNING: Could not put all atoms in the compact unitcell\n"
: NULL;
}
开发者ID:alexholehouse，项目名称:gromacs，代码行数:19，代码来源:pbc.c
示例17: calc_dist
static void calc_dist(int nind, int index[], const rvec x[], int ePBC, matrix box,
real **d)
{
int i, j;
rvec dx;
real temp2;
t_pbc pbc;
set_pbc(&pbc, ePBC, box);
for (i = 0; (i < nind-1); i++)
{
const real *xi = x[index[i]];
for (j = i+1; (j < nind); j++)
{
pbc_dx(&pbc, xi, x[index[j]], dx);
temp2 = norm2(dx);
d[i][j] = std::sqrt(temp2);
}
}
}
开发者ID:MichalKononenko，项目名称:gromacs，代码行数:20，代码来源:gmx_rmsdist.cpp
示例18: put_atoms_in_compact_unitcell
void put_atoms_in_compact_unitcell(int ePBC, int ecenter, const matrix box,
int natoms, rvec x[])
{
t_pbc pbc;
rvec box_center, dx;
int i;
set_pbc(&pbc, ePBC, box);
if (pbc.ePBCDX == epbcdxUNSUPPORTED)
{
gmx_fatal(FARGS, "Can not put atoms in compact unitcell with unsupported PBC");
}
calc_box_center(ecenter, box, box_center);
for (i = 0; i < natoms; i++)
{
pbc_dx(&pbc, x[i], box_center, dx);
rvec_add(box_center, dx, x[i]);
}
}
开发者ID:wangxubo0201，项目名称:gromacs，代码行数:21，代码来源:pbc.cpp
示例19: gmx_calc_cog_pbc
/*!
* \param[in] top Topology structure (unused, can be NULL).
* \param[in] x Position vectors of all atoms.
* \param[in] pbc Periodic boundary conditions structure.
* \param[in] nrefat Number of atoms in the index.
* \param[in] index Indices of atoms.
* \param[out] xout COG position for the indexed atoms.
*
* Works exactly as gmx_calc_com_pbc(), but calculates the center of geometry.
*/
void
gmx_calc_cog_pbc(const gmx_mtop_t *top, rvec x[], const t_pbc *pbc,
int nrefat, const int index[], rvec xout)
{
const real tol = 1e-4;
bool bChanged;
int m, j, ai, iter;
rvec dx, xtest;
/* First simple calculation */
gmx_calc_cog(top, x, nrefat, index, xout);
/* Now check if any atom is more than half the box from the COM */
if (pbc)
{
iter = 0;
do
{
bChanged = false;
for (m = 0; m < nrefat; ++m)
{
ai = index[m];
pbc_dx(pbc, x[ai], xout, dx);
rvec_add(xout, dx, xtest);
for (j = 0; j < DIM; ++j)
{
if (fabs(xtest[j] - x[ai][j]) > tol)
{
/* Here we have used the wrong image for contributing to the COM */
xout[j] += (xtest[j] - x[ai][j]) / nrefat;
x[ai][j] = xtest[j];
bChanged = true;
}
}
}
iter++;
}
while (bChanged);
}
}
开发者ID:MrTheodor，项目名称:gromacs，代码行数:49，代码来源:centerofmass.cpp
示例20: adress_weight
real
adress_weight(rvec x,
int adresstype,
real adressr,
real adressw,
rvec * ref,
t_pbc * pbc,
t_forcerec * fr )
{
int i;
real l2 = adressr+adressw;
real sqr_dl, dl;
real tmp;
rvec dx;
sqr_dl = 0.0;
if (pbc)
{
pbc_dx(pbc, (*ref), x, dx);
}
else
{
rvec_sub((*ref), x, dx);
}
switch (adresstype)
{
case eAdressOff:
/* default to explicit simulation */
return 1;
case eAdressConst:
/* constant value for weighting function = adressw */
return fr->adress_const_wf;
case eAdressXSplit:
/* plane through center of ref, varies in x direction */
sqr_dl = dx[0]*dx[0];
break;
case eAdressSphere:
/* point at center of ref, assuming cubic geometry */
for (i = 0; i < 3; i++)
{
sqr_dl += dx[i]*dx[i];
}
break;
default:
/* default to explicit simulation */
return 1;
}
dl = sqrt(sqr_dl);
/* molecule is coarse grained */
if (dl > l2)
{
return 0;
}
/* molecule is explicit */
else if (dl < adressr)
{
return 1;
}
/* hybrid region */
else
{
tmp = cos((dl-adressr)*M_PI/2/adressw);
return tmp*tmp;
}
}
开发者ID:exianshine，项目名称:gromacs，代码行数:69，代码来源:adress.c
注：本文中的pbc_dx函数示例由纯净天空整理自Github/MSDocs等源码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。 |
客服电话
APP下载
官方微信
请发表评论