void apbsnlinduce_(double uinp[maxatm][3], double fld[maxatm][3]){
/* Misc. pointers to APBS data structures */
Vpmg *pmg[NOSH_MAXCALC];
Vpmgp *pmgp[NOSH_MAXCALC];
Vpbe *pbe[NOSH_MAXCALC];
MGparm *mgparm = VNULL;
PBEparm *pbeparm = VNULL;
Vatom *atom = VNULL;
/* Observables and unit conversion */
double field[3];
double sign,kT,electric;
/* Potential Vgrid construction */
double nx,ny,nz,hx,hy,hzed,xmin,ymin,zmin;
double *data;
/* Loop variables */
int i,j;
VASSERT(nosh != VNULL);
for (i=0; i<NOSH_MAXCALC; i++) {
pmg[i] = VNULL;
pmgp[i] = VNULL;
pbe[i] = VNULL;
}
/* Read TINKER induce input data into Vatom instances. */
for (i=0; i < alist[0]->number; i++){
atom = Valist_getAtom(alist[0],i);
Vatom_setNLInducedDipole(atom, uinp[i]);
for (j=0;j<3;j++){
fld[i][j] = 0.0;
}
}
/* Solve the LPBE for the homogeneous system, then solvated. */
for (i=0; i<2; i++) {
pmg[i] = VNULL;
pmgp[i] = VNULL;
pbe[i] = VNULL;
/* Useful local variables */
mgparm = nosh->calc[i]->mgparm;
pbeparm = nosh->calc[i]->pbeparm;
if (!MGparm_check(mgparm)){
printf("MGparm Check failed\n");
exit(-1);
}
if (!PBEparm_check(pbeparm)){
printf("PBEparm Check failed\n");
exit(-1);
}
/* Set up problem */
mgparm->chgs = VCM_NLINDUCED;
if (!initMG(i, nosh, mgparm, pbeparm, realCenter, pbe,
alist, dielXMap, dielYMap, dielZMap,
kappaMap, chargeMap, pmgp, pmg, potMap)) {
Vnm_tprint( 2, "Error setting up MG calculation!\n");
return;
}
/* Solve the PDE */
if (solveMG(nosh, pmg[i], mgparm->type) != 1) {
Vnm_tprint(2, "Error solving PDE!\n");
return;
}
/* Set partition information for observables and I/O */
if (setPartMG(nosh, mgparm, pmg[i]) != 1) {
Vnm_tprint(2, "Error setting partition info!\n");
return;
}
/* Save the potential due to non-local induced dipoles */
nx = pmg[i]->pmgp->nx;
ny = pmg[i]->pmgp->ny;
nz = pmg[i]->pmgp->nz;
hx = pmg[i]->pmgp->hx;
hy = pmg[i]->pmgp->hy;
hzed = pmg[i]->pmgp->hzed;
xmin = pmg[i]->pmgp->xmin;
ymin = pmg[i]->pmgp->ymin;
zmin = pmg[i]->pmgp->zmin;
if (nlIndU[i] == VNULL) {
data = Vmem_malloc(VNULL, nx*ny*nz, sizeof(double));
Vpmg_fillArray(pmg[i], data, VDT_POT, 0.0, pbeparm->pbetype, pbeparm);
nlIndU[i] = Vgrid_ctor(nx,ny,nz,hx,hy,hzed,xmin,ymin,zmin,data);
nlIndU[i]->readdata = 1; // set readata flag to have dtor free data
} else {
data = nlIndU[i]->data;
Vpmg_fillArray(pmg[i], data, VDT_POT, 0.0, pbeparm->pbetype, pbeparm);
}
if (i == 0){
sign = -1.0;
} else {
sign = 1.0;
}
for (j=0; j < alist[0]->number; j++){
Vpmg_fieldSpline4(pmg[i], j, field);
fld[j][0] += sign * field[0];
fld[j][1] += sign * field[1];
fld[j][2] += sign * field[2];
}
}
/* load results into the return arrays in electron**2/Angstrom
/* kT in kcal/mol */
kT = Vunit_kb * (1e-3) * Vunit_Na * 298.15 / 4.184;
// electric: conversion from electron**2/Angstrom to Kcal/mol
electric = 332.063709;
for (i=0; i<alist[0]->number; i++){
fld[i][0] *= kT / electric;
fld[i][1] *= kT / electric;
fld[i][2] *= kT / electric;
}
killMG(nosh, pbe, pmgp, pmg);
}
int main(int argc, char *argv[])
{
std::cout<<"Your Alias: "<< "Ang_Wang"<<std::endl;
//READING IN FROM TERMINAL
int l;
if(argc!=1)
l = atoi(argv[1]);
else
l = 11;
//FOR OUTPUT
std::ofstream init;
init.open("init.dat");
std::ofstream solution;
solution.open("solution.dat");
//DEFINITION OF PARAMETERS
std::size_t grid_size = pow(2,l)+1;
double h = 2.0/((double) (grid_size-1));
std::size_t grid_size_x = grid_size;
std::size_t grid_size_y = (grid_size - 1)/2 + 1;
//STORING AND PRINTING THE ENTIRE VELOCITY DIST
std::vector<std::vector<double > > u(grid_size_y, std::vector<double>(grid_size_x));
init_and_boundary(u);
std::vector<std::vector<double > > f(grid_size_y, std::vector<double>(grid_size_x));
for (std::size_t i=0;i<grid_size_y;++i){
for (std::size_t j=0;j<grid_size_x;++j){
init<<std::setw(10)<<(j*h-1)<<" "<<std::setw(10)<<(1-i*h)<<" "<<std::setw(10)<<u[i][j]<<std::endl;
}
}
for (std::size_t i=0; i<grid_size_y-1 ;++i){
for (std::size_t j=0;j<grid_size_x;++j){
init<<std::setw(10)<<(j*h-1)<<" "<<std::setw(10)<<(-1+i*h)<<" "<<std::setw(10)<<u[i][j]<<std::endl;
}
}
init.close();
//TO MEASURE THE WALL CLOCK TIME
struct timeval t0, t;
gettimeofday(&t0, NULL);
solveMG(l, u, f);
//MEASURE WALL CLOCK TIME THE PROGRAMME TAKES
gettimeofday(&t, NULL);
std::cout<<"Wall clock time of MG execution: "<< ((int64_t)(t.tv_sec - t0.tv_sec) * (int64_t) 1000000 + (int64_t)t.tv_usec - (int64_t)t0.tv_usec) * 1e-3 << " ms"<<std::endl;
// WRITING THE COMPUTED SOLUTION TO A FILE NAMED SOLUTION.TXT
for (std::size_t i=0;i<grid_size_y;++i){
for (std::size_t j=0;j<grid_size_x;++j){
solution<<std::setw(10)<<(j*h-1)<<" "<<std::setw(10)<<(1-i*h)<<" "<<std::setw(10)<<u[i][j]<<std::endl;
}
}
for (std::size_t i=0; i<grid_size_y-1 ;++i){
for (std::size_t j=0;j<grid_size_x;++j){
solution<<std::setw(10)<<(j*h-1)<<" "<<std::setw(10)<<(-1+i*h)<<" "<<std::setw(10)<<u[i][j]<<std::endl;
}
}
solution.close();
}
void apbsempole_(int *natom, double x[maxatm][3],
double rad[maxatm], double rpole[maxatm][13],
double *total,
double energy[maxatm], double fld[maxatm][3],
double rff[maxatm][3], double rft[maxatm][3]) {
/* Misc. pointers to APBS data structures */
Vpmg *pmg[NOSH_MAXCALC];
Vpmgp *pmgp[NOSH_MAXCALC];
Vpbe *pbe[NOSH_MAXCALC];
MGparm *mgparm = VNULL;
PBEparm *pbeparm = VNULL;
Vatom *atom = VNULL;
/* Vgrid configuration for the kappa and dielectric maps */
double nx,ny,nz,hx,hy,hzed,xmin,ymin,zmin;
double *data;
double zkappa2, epsp, epsw;
/* Loop indeces */
int i,j;
/* Observables and unit conversion */
double sign, force[3], torque[3], field[3];
double kT,electric,debye;
double charge, dipole[3], quad[9];
debye = 4.8033324;
for (i=0; i<NOSH_MAXCALC; i++) {
pmg[i] = VNULL;
pmgp[i] = VNULL;
pbe[i] = VNULL;
}
/* Kill the saved potential Vgrids */
for (i=0; i<2; i++){
if (permU[i] != VNULL) Vgrid_dtor(&permU[i]);
if (indU[i] != VNULL) Vgrid_dtor(&indU[i]);
if (nlIndU[i] != VNULL) Vgrid_dtor(&nlIndU[i]);
}
/* Kill the old atom list */
if (alist[0] != VNULL) {
Valist_dtor(&alist[0]);
}
/* Create a new atom list (mol == 1) */
if (alist[0] == VNULL) {
alist[0] = Valist_ctor();
alist[0]->atoms = Vmem_malloc(alist[0]->vmem, *natom, (sizeof(Vatom)));
alist[0]->number = *natom;
}
/* Read TINKER input data into Vatom instances. */
for (i=0; i < alist[0]->number; i++){
atom = Valist_getAtom(alist[0],i);
Vatom_setAtomID(atom, i);
Vatom_setPosition(atom, x[i]);
Vatom_setRadius(atom, rad[i]);
charge = rpole[i][0];
Vatom_setCharge(atom, charge);
dipole[0] = rpole[i][1];
dipole[1] = rpole[i][2];
dipole[2] = rpole[i][3];
Vatom_setDipole(atom, dipole);
quad[0] = rpole[i][4];
quad[1] = rpole[i][5];
quad[2] = rpole[i][6];
quad[3] = rpole[i][7];
quad[4] = rpole[i][8];
quad[5] = rpole[i][9];
quad[6] = rpole[i][10];
quad[7] = rpole[i][11];
quad[8] = rpole[i][12];
Vatom_setQuadrupole(atom, quad);
/* Useful check
printf(" %i %f (%f,%f,%f)\n",i,rad[i], x[i][0], x[i][1], x[i][2]);
printf(" %f\n %f,%f,%f\n", charge, dipole[0], dipole[1], dipole[2]);
printf(" %f\n", quad[0]);
printf(" %f %f\n", quad[3], quad[4]);
printf(" %f %f %f\n", quad[6], quad[7], quad[8]); */
energy[i] = 0.0;
for (j=0;j<3;j++){
fld[i][j] = 0.0;
rff[i][j] = 0.0;
rft[i][j] = 0.0;
}
}
nosh->nmol = 1;
Valist_getStatistics(alist[0]);
/* Only call the setupCalc routine once, so that we can
reuse this nosh object */
if (nosh->ncalc < 2) {
if (NOsh_setupElecCalc(nosh, alist) != 1) {
printf("Error setting up calculations\n");
exit(-1);
}
}
/* Solve the LPBE for the homogeneous and then solvated states */
for (i=0; i<2; i++) {
/* Useful local variables */
mgparm = nosh->calc[i]->mgparm;
pbeparm = nosh->calc[i]->pbeparm;
/* Just to be robust */
if (!MGparm_check(mgparm)){
printf("MGparm Check failed\n");
printMGPARM(mgparm, realCenter);
exit(-1);
}
if (!PBEparm_check(pbeparm)){
printf("PBEparm Check failed\n");
printPBEPARM(pbeparm);
exit(-1);
}
/* Set up the problem */
mgparm->chgs = VCM_PERMANENT;
if (!initMG(i, nosh, mgparm, pbeparm, realCenter, pbe,
alist, dielXMap, dielYMap, dielZMap,
kappaMap, chargeMap, pmgp, pmg, potMap)) {
Vnm_tprint( 2, "Error setting up MG calculation!\n");
return;
}
/* Solve the PDE */
if (solveMG(nosh, pmg[i], mgparm->type) != 1) {
Vnm_tprint(2, "Error solving PDE!\n");
return;
}
/* Set partition information for observables and I/O */
/* Note - parallel operation has NOT been tested. */
if (setPartMG(nosh, mgparm, pmg[i]) != 1) {
Vnm_tprint(2, "Error setting partition info!\n");
return;
}
nx = pmg[i]->pmgp->nx;
ny = pmg[i]->pmgp->ny;
nz = pmg[i]->pmgp->nz;
hx = pmg[i]->pmgp->hx;
hy = pmg[i]->pmgp->hy;
hzed = pmg[i]->pmgp->hzed;
xmin = pmg[i]->pmgp->xmin;
ymin = pmg[i]->pmgp->ymin;
zmin = pmg[i]->pmgp->zmin;
/* Save dielectric/kappa maps into Vgrids, then change the nosh
* data structure to think it read these maps in from a file.
* The goal is to save setup time during convergence of the
* induced dipoles. This is under consideration...
* */
/*
// X (shifted)
data = Vmem_malloc(mem, nx*ny*nz, sizeof(double));
Vpmg_fillArray(pmg[i], data, VDT_DIELX, 0.0, pbeparm->pbetype);
dielXMap[i] = Vgrid_ctor(nx,ny,nz,hx,hy,hzed,
xmin + 0.5*hx,ymin,zmin,data);
dielXMap[i]->readdata = 1;
// Y (shifted)
data = Vmem_malloc(mem, nx*ny*nz, sizeof(double));
Vpmg_fillArray(pmg[i], data, VDT_DIELY, 0.0, pbeparm->pbetype);
dielYMap[i] = Vgrid_ctor(nx,ny,nz,hx,hy,hzed,
xmin,ymin + 0.5*hy,zmin,data);
dielYMap[i]->readdata = 1;
// Z (shifted)
data = Vmem_malloc(mem, nx*ny*nz, sizeof(double));
Vpmg_fillArray(pmg[i], data, VDT_DIELZ, 0.0, pbeparm->pbetype);
dielZMap[i] = Vgrid_ctor(nx,ny,nz,hx,hy,hzed,
xmin,ymin,zmin + 0.5*hzed,data);
dielZMap[i]->readdata = 1;
// Kappa
data = Vmem_malloc(mem, nx*ny*nz, sizeof(double));
Vpmg_fillArray(pmg[i], data, VDT_KAPPA, 0.0, pbeparm->pbetype);
kappaMap[i] = Vgrid_ctor(nx,ny,nz,hx,hy,hzed,xmin,ymin,zmin,data);
kappaMap[i]->readdata = 1;
// Update the pbeparam structure, since we now have
// dielectric and kappap maps
pbeparm->useDielMap = 1;
pbeparm->dielMapID = i + 1;
pbeparm->useKappaMap = 1;
pbeparm->kappaMapID = i + 1;
*/
data = Vmem_malloc(mem, nx*ny*nz, sizeof(double));
Vpmg_fillArray(pmg[i], data, VDT_POT, 0.0, pbeparm->pbetype, pbeparm);
permU[i] = Vgrid_ctor(nx,ny,nz,hx,hy,hzed,xmin,ymin,zmin,data);
permU[i]->readdata = 1;
// set readdata flag to have the dtor to free data
if (i == 0){
sign = -1.0;
} else {
sign = 1.0;
}
/* Calculate observables */
for (j=0; j < alist[0]->number; j++){
energy[j] += sign * Vpmg_qfPermanentMultipoleEnergy(pmg[i], j);
Vpmg_fieldSpline4(pmg[i], j, field);
fld[j][0] += sign * field[0];
fld[j][1] += sign * field[1];
fld[j][2] += sign * field[2];
}
if (!pmg[i]->pmgp->nonlin &&
(pmg[i]->surfMeth == VSM_SPLINE ||
pmg[i]->surfMeth == VSM_SPLINE3 ||
pmg[i]->surfMeth == VSM_SPLINE4)) {
for (j=0; j < alist[0]->number; j++){
Vpmg_qfPermanentMultipoleForce(pmg[i], j, force, torque);
rff[j][0] += sign * force[0];
rff[j][1] += sign * force[1];
rff[j][2] += sign * force[2];
rft[j][0] += sign * torque[0];
rft[j][1] += sign * torque[1];
rft[j][2] += sign * torque[2];
}
kT = Vunit_kb * (1e-3) * Vunit_Na * 298.15 * 1.0/4.184;
epsp = Vpbe_getSoluteDiel(pmg[i]->pbe);
epsw = Vpbe_getSolventDiel(pmg[i]->pbe);
if (VABS(epsp-epsw) > VPMGSMALL) {
for (j=0; j < alist[0]->number; j++){
Vpmg_dbPermanentMultipoleForce(pmg[i], j, force);
rff[j][0] += sign * force[0];
rff[j][1] += sign * force[1];
rff[j][2] += sign * force[2];
}
}
zkappa2 = Vpbe_getZkappa2(pmg[i]->pbe);
if (zkappa2 > VPMGSMALL) {
for (j=0; j < alist[0]->number; j++) {
Vpmg_ibPermanentMultipoleForce(pmg[i], j, force);
rff[j][0] += sign * force[0];
rff[j][1] += sign * force[1];
rff[j][2] += sign * force[2];
}
}
}
}
//nosh->ndiel = 2;
//nosh->nkappa = 2;
/*
printf("Energy (multipole) %f Kcal/mol\n", *energy);
printf("Energy (volume) %f Kcal/mol\n", evol * 0.5 * kT);
*/
// Convert results into kcal/mol units
kT = Vunit_kb * (1e-3) * Vunit_Na * 298.15 * 1.0/4.184;
// Electric converts from electron**2/Angstrom to kcal/mol
electric = 332.063709;
*total = 0.0;
for (i=0; i<alist[0]->number; i++){
/* starting with the field in KT/e/Ang^2 multiply by kcal/mol/KT
the field is then divided by "electric" to convert to e/Ang^2 */
energy[i] *= 0.5 * kT;
*total += energy[i];
fld[i][0] *= kT / electric;
fld[i][1] *= kT / electric;
fld[i][2] *= kT / electric;
rff[i][0] *= kT;
rff[i][1] *= kT;
rff[i][2] *= kT;
rft[i][0] *= kT;
rft[i][1] *= kT;
rft[i][2] *= kT;
}
killMG(nosh, pbe, pmgp, pmg);
}