void sum_lrforces(rvec f[],t_forcerec *fr,int start,int homenr)
{
/* Now add the forces from the PME calculation. Since this only produces
* forces on the local atoms, this can be safely done after the
* communication step.
*/
if (EEL_LR(fr->eeltype))
sum_forces(start,start+homenr,f,fr->f_pme);
}
void do_force(FILE *fplog,t_commrec *cr,
t_inputrec *inputrec,
int step,t_nrnb *nrnb,gmx_wallcycle_t wcycle,
gmx_localtop_t *top,
gmx_groups_t *groups,
matrix box,rvec x[],history_t *hist,
rvec f[],rvec buf[],
tensor vir_force,
t_mdatoms *mdatoms,
gmx_enerdata_t *enerd,t_fcdata *fcd,
real lambda,t_graph *graph,
t_forcerec *fr,gmx_vsite_t *vsite,rvec mu_tot,
real t,FILE *field,gmx_edsam_t ed,
int flags)
{
static rvec box_size;
int cg0,cg1,i,j;
int start,homenr;
static double mu[2*DIM];
rvec mu_tot_AB[2];
bool bSepDVDL,bStateChanged,bNS,bFillGrid,bCalcCGCM,bBS,bDoForces;
matrix boxs;
real e,v,dvdl;
t_pbc pbc;
float cycles_ppdpme,cycles_pme,cycles_force;
start = mdatoms->start;
homenr = mdatoms->homenr;
bSepDVDL = (fr->bSepDVDL && do_per_step(step,inputrec->nstlog));
clear_mat(vir_force);
if (PARTDECOMP(cr)) {
pd_cg_range(cr,&cg0,&cg1);
} else {
cg0 = 0;
if (DOMAINDECOMP(cr))
cg1 = cr->dd->ncg_tot;
else
cg1 = top->cgs.nr;
if (fr->n_tpi > 0)
cg1--;
}
bStateChanged = (flags & GMX_FORCE_STATECHANGED);
bNS = (flags & GMX_FORCE_NS);
bFillGrid = (bNS && bStateChanged);
bCalcCGCM = (bFillGrid && !DOMAINDECOMP(cr));
bDoForces = (flags & GMX_FORCE_FORCES);
if (bStateChanged) {
update_forcerec(fplog,fr,box);
/* Calculate total (local) dipole moment in a temporary common array.
* This makes it possible to sum them over nodes faster.
*/
calc_mu(start,homenr,
x,mdatoms->chargeA,mdatoms->chargeB,mdatoms->nChargePerturbed,
mu,mu+DIM);
}
if (fr->ePBC != epbcNONE) {
/* Compute shift vectors every step,
* because of pressure coupling or box deformation!
*/
if (DYNAMIC_BOX(*inputrec) && bStateChanged)
calc_shifts(box,fr->shift_vec);
if (bCalcCGCM) {
put_charge_groups_in_box(fplog,cg0,cg1,fr->ePBC,box,
&(top->cgs),x,fr->cg_cm);
inc_nrnb(nrnb,eNR_CGCM,homenr);
inc_nrnb(nrnb,eNR_RESETX,cg1-cg0);
}
else if (EI_ENERGY_MINIMIZATION(inputrec->eI) && graph) {
unshift_self(graph,box,x);
}
}
else if (bCalcCGCM) {
calc_cgcm(fplog,cg0,cg1,&(top->cgs),x,fr->cg_cm);
inc_nrnb(nrnb,eNR_CGCM,homenr);
}
if (bCalcCGCM) {
if (PAR(cr)) {
move_cgcm(fplog,cr,fr->cg_cm);
}
if (gmx_debug_at)
pr_rvecs(debug,0,"cgcm",fr->cg_cm,top->cgs.nr);
}
#ifdef GMX_MPI
if (!(cr->duty & DUTY_PME)) {
/* Send particle coordinates to the pme nodes.
* Since this is only implemented for domain decomposition
* and domain decomposition does not use the graph,
* we do not need to worry about shifting.
*/
wallcycle_start(wcycle,ewcPP_PMESENDX);
GMX_MPE_LOG(ev_send_coordinates_start);
bBS = (inputrec->nwall == 2);
if (bBS) {
copy_mat(box,boxs);
svmul(inputrec->wall_ewald_zfac,boxs[ZZ],boxs[ZZ]);
}
gmx_pme_send_x(cr,bBS ? boxs : box,x,mdatoms->nChargePerturbed,lambda);
GMX_MPE_LOG(ev_send_coordinates_finish);
wallcycle_stop(wcycle,ewcPP_PMESENDX);
}
#endif /* GMX_MPI */
/* Communicate coordinates and sum dipole if necessary */
if (PAR(cr)) {
wallcycle_start(wcycle,ewcMOVEX);
if (DOMAINDECOMP(cr)) {
dd_move_x(cr->dd,box,x,buf);
} else {
move_x(fplog,cr,GMX_LEFT,GMX_RIGHT,x,nrnb);
}
/* When we don't need the total dipole we sum it in global_stat */
if (NEED_MUTOT(*inputrec))
gmx_sumd(2*DIM,mu,cr);
wallcycle_stop(wcycle,ewcMOVEX);
}
for(i=0; i<2; i++)
for(j=0;j<DIM;j++)
mu_tot_AB[i][j] = mu[i*DIM + j];
if (fr->efep == efepNO)
copy_rvec(mu_tot_AB[0],mu_tot);
else
for(j=0; j<DIM; j++)
mu_tot[j] = (1.0 - lambda)*mu_tot_AB[0][j] + lambda*mu_tot_AB[1][j];
/* Reset energies */
reset_energies(&(inputrec->opts),fr,bNS,enerd,MASTER(cr));
if (bNS) {
wallcycle_start(wcycle,ewcNS);
if (graph && bStateChanged)
/* Calculate intramolecular shift vectors to make molecules whole */
mk_mshift(fplog,graph,fr->ePBC,box,x);
/* Reset long range forces if necessary */
if (fr->bTwinRange) {
clear_rvecs(fr->f_twin_n,fr->f_twin);
clear_rvecs(SHIFTS,fr->fshift_twin);
}
/* Do the actual neighbour searching and if twin range electrostatics
* also do the calculation of long range forces and energies.
*/
dvdl = 0;
ns(fplog,fr,x,f,box,groups,&(inputrec->opts),top,mdatoms,
cr,nrnb,step,lambda,&dvdl,&enerd->grpp,bFillGrid,bDoForces);
if (bSepDVDL)
fprintf(fplog,sepdvdlformat,"LR non-bonded",0,dvdl);
enerd->dvdl_lr = dvdl;
enerd->term[F_DVDL] += dvdl;
wallcycle_stop(wcycle,ewcNS);
}
if (DOMAINDECOMP(cr)) {
if (!(cr->duty & DUTY_PME)) {
wallcycle_start(wcycle,ewcPPDURINGPME);
dd_force_flop_start(cr->dd,nrnb);
}
}
/* Start the force cycle counter.
* This counter is stopped in do_forcelow_level.
* No parallel communication should occur while this counter is running,
* since that will interfere with the dynamic load balancing.
*/
wallcycle_start(wcycle,ewcFORCE);
if (bDoForces) {
/* Reset PME/Ewald forces if necessary */
if (fr->bF_NoVirSum)
{
GMX_BARRIER(cr->mpi_comm_mygroup);
if (fr->bDomDec)
clear_rvecs(fr->f_novirsum_n,fr->f_novirsum);
else
clear_rvecs(homenr,fr->f_novirsum+start);
GMX_BARRIER(cr->mpi_comm_mygroup);
}
/* Copy long range forces into normal buffers */
if (fr->bTwinRange) {
for(i=0; i<fr->f_twin_n; i++)
copy_rvec(fr->f_twin[i],f[i]);
for(i=0; i<SHIFTS; i++)
copy_rvec(fr->fshift_twin[i],fr->fshift[i]);
}
else {
if (DOMAINDECOMP(cr))
clear_rvecs(cr->dd->nat_tot,f);
else
clear_rvecs(mdatoms->nr,f);
clear_rvecs(SHIFTS,fr->fshift);
}
clear_rvec(fr->vir_diag_posres);
GMX_BARRIER(cr->mpi_comm_mygroup);
}
if (inputrec->ePull == epullCONSTRAINT)
clear_pull_forces(inputrec->pull);
/* update QMMMrec, if necessary */
if(fr->bQMMM)
update_QMMMrec(cr,fr,x,mdatoms,box,top);
if ((flags & GMX_FORCE_BONDED) && top->idef.il[F_POSRES].nr > 0) {
/* Position restraints always require full pbc */
set_pbc(&pbc,inputrec->ePBC,box);
v = posres(top->idef.il[F_POSRES].nr,top->idef.il[F_POSRES].iatoms,
top->idef.iparams_posres,
(const rvec*)x,fr->f_novirsum,fr->vir_diag_posres,
inputrec->ePBC==epbcNONE ? NULL : &pbc,lambda,&dvdl,
fr->rc_scaling,fr->ePBC,fr->posres_com,fr->posres_comB);
if (bSepDVDL) {
fprintf(fplog,sepdvdlformat,
interaction_function[F_POSRES].longname,v,dvdl);
}
enerd->term[F_POSRES] += v;
enerd->term[F_DVDL] += dvdl;
inc_nrnb(nrnb,eNR_POSRES,top->idef.il[F_POSRES].nr/2);
}
/* Compute the bonded and non-bonded forces */
do_force_lowlevel(fplog,step,fr,inputrec,&(top->idef),
cr,nrnb,wcycle,mdatoms,&(inputrec->opts),
x,hist,f,enerd,fcd,box,lambda,graph,&(top->excls),mu_tot_AB,
flags,&cycles_force);
GMX_BARRIER(cr->mpi_comm_mygroup);
if (ed) {
do_flood(fplog,cr,x,f,ed,box,step);
}
if (DOMAINDECOMP(cr)) {
dd_force_flop_stop(cr->dd,nrnb);
if (wcycle)
dd_cycles_add(cr->dd,cycles_force,ddCyclF);
}
if (bDoForces) {
/* Compute forces due to electric field */
calc_f_el(MASTER(cr) ? field : NULL,
start,homenr,mdatoms->chargeA,x,f,inputrec->ex,inputrec->et,t);
/* When using PME/Ewald we compute the long range virial there.
* otherwise we do it based on long range forces from twin range
* cut-off based calculation (or not at all).
*/
/* Communicate the forces */
if (PAR(cr)) {
wallcycle_start(wcycle,ewcMOVEF);
if (DOMAINDECOMP(cr)) {
dd_move_f(cr->dd,f,buf,fr->fshift);
/* Position restraint do not introduce inter-cg forces */
if (EEL_FULL(fr->eeltype) && cr->dd->n_intercg_excl)
dd_move_f(cr->dd,fr->f_novirsum,buf,NULL);
} else {
move_f(fplog,cr,GMX_LEFT,GMX_RIGHT,f,buf,nrnb);
}
wallcycle_stop(wcycle,ewcMOVEF);
}
}
if (bDoForces) {
if (vsite) {
wallcycle_start(wcycle,ewcVSITESPREAD);
spread_vsite_f(fplog,vsite,x,f,fr->fshift,nrnb,
&top->idef,fr->ePBC,fr->bMolPBC,graph,box,cr);
wallcycle_stop(wcycle,ewcVSITESPREAD);
}
/* Calculation of the virial must be done after vsites! */
calc_virial(fplog,mdatoms->start,mdatoms->homenr,x,f,
vir_force,graph,box,nrnb,fr,inputrec->ePBC);
}
if (inputrec->ePull == epullUMBRELLA || inputrec->ePull == epullCONST_F) {
/* Calculate the center of mass forces, this requires communication,
* which is why pull_potential is called close to other communication.
* The virial contribution is calculated directly,
* which is why we call pull_potential after calc_virial.
*/
set_pbc(&pbc,inputrec->ePBC,box);
dvdl = 0;
enerd->term[F_COM_PULL] =
pull_potential(inputrec->ePull,inputrec->pull,mdatoms,&pbc,
cr,t,lambda,x,f,vir_force,&dvdl);
if (bSepDVDL)
fprintf(fplog,sepdvdlformat,"Com pull",enerd->term[F_COM_PULL],dvdl);
enerd->term[F_DVDL] += dvdl;
}
if (!(cr->duty & DUTY_PME)) {
cycles_ppdpme = wallcycle_stop(wcycle,ewcPPDURINGPME);
dd_cycles_add(cr->dd,cycles_ppdpme,ddCyclPPduringPME);
}
#ifdef GMX_MPI
if (PAR(cr) && !(cr->duty & DUTY_PME)) {
/* In case of node-splitting, the PP nodes receive the long-range
* forces, virial and energy from the PME nodes here.
*/
wallcycle_start(wcycle,ewcPP_PMEWAITRECVF);
dvdl = 0;
gmx_pme_receive_f(cr,fr->f_novirsum,fr->vir_el_recip,&e,&dvdl,
&cycles_pme);
if (bSepDVDL)
fprintf(fplog,sepdvdlformat,"PME mesh",e,dvdl);
enerd->term[F_COUL_RECIP] += e;
enerd->term[F_DVDL] += dvdl;
if (wcycle)
dd_cycles_add(cr->dd,cycles_pme,ddCyclPME);
wallcycle_stop(wcycle,ewcPP_PMEWAITRECVF);
}
#endif
if (bDoForces && fr->bF_NoVirSum) {
if (vsite) {
/* Spread the mesh force on virtual sites to the other particles...
* This is parallellized. MPI communication is performed
* if the constructing atoms aren't local.
*/
wallcycle_start(wcycle,ewcVSITESPREAD);
spread_vsite_f(fplog,vsite,x,fr->f_novirsum,NULL,nrnb,
&top->idef,fr->ePBC,fr->bMolPBC,graph,box,cr);
wallcycle_stop(wcycle,ewcVSITESPREAD);
}
/* Now add the forces, this is local */
if (fr->bDomDec) {
sum_forces(0,fr->f_novirsum_n,f,fr->f_novirsum);
} else {
sum_forces(start,start+homenr,f,fr->f_novirsum);
}
if (EEL_FULL(fr->eeltype)) {
/* Add the mesh contribution to the virial */
m_add(vir_force,fr->vir_el_recip,vir_force);
}
if (debug)
pr_rvecs(debug,0,"vir_force",vir_force,DIM);
}
/* Sum the potential energy terms from group contributions */
sum_epot(&(inputrec->opts),enerd);
if (fr->print_force >= 0 && bDoForces)
print_large_forces(stderr,mdatoms,cr,step,fr->print_force,x,f);
}
/*_________________________________Main body__________________________________*/
void main(void)
{
double free_particle[n_max][m_max][z_max];
/*This is the array which holds*/
/*the properties of all of the */
/*free_particles in the system */
double image_free_particle[n_max][m_max][z_max];
/*This is the array which holds*/
/*the properties of all of the */
/*images of the free_particles */
/*in the system */
double wall_particle[44][m_max][z_max];
/*This is the array which holds */
/*the properties of all of the */
/*wall_particles in the system */
double free_forces[n_max][n_max][z_max];
/*Contains values of forces */
/*between free_particle pairs*/
double image_free_forces[n_max][n_max][z_max];
/*Contains values of forces*/
/*between free and image */
/*particle pairs */
double image_image_forces[n_max][n_max][z_max];
/*Contains values of forces*/
/*between image particle */
/*pairs */
double wall_free_forces[n_max][44][z_max];
/*Contains values of forces between*/
/*wall and free particle pairs */
double wall_image_forces[n_max][44][z_max];
/*Contains values of forces between*/
/*wall and image particle pairs */
double x[n_max][n_max];
/*Contains the overlap dist*/
/*between free_particle pairs*/
double image_x[n_max][n_max];
/*Contains the overlap dist*/
/*between free and image */
/*particle pairs */
double wall_x[n_max][44];
/*Contains the overlap dist*/
/*between wall and free */
/*particle pairs */
double image_image_x[n_max][n_max];
/*Contains the overlap dist*/
/*between two image */
/*particle pairs */
double wall_image_x[n_max][44];
/*Contains the overlap dist*/
/*between wall and image */
/*particle pairs */
double t = t_min;
/*Timer for simulation*/
/*Energy Variables*/
double kinetic_energy,potential_energy,total_energy;
/*Counters*/
int i,k;
int j = 0;
int l = 0;
/*Average Radius*/
double rad;
/*Packing density*/
double packing;
/*Average Coordiantion Number*/
double coord_number;
/*Average Velocity*/
double average_vel_x;
double average_vel_y;
#include"incl/files.h"
#include"incl/includes.h"
/*____________________________________________________________________________*/
/*_____________________________Execute the program____________________________*/
/*____________________________________________________________________________*/
ERR_MSG r;
/*Set the initial properties of the free_particles*/
initiate(free_particle,image_free_particle,wall_particle,
free_forces,image_free_forces,wall_free_forces,
image_image_forces,wall_image_forces,x,image_x,
wall_x,image_image_x,wall_image_x);
printf("Initialising\n");
/*____________________________________________________________________________*/
/*Assign free particles radii randomly*/
printf("Assigning");
rad = set_free_radii(free_particle);
fprintf(fptr3,"%lf\n",rad);
printf("Setting free particle radii\n");
/*____________________________________________________________________________*/
/*Assign free particles their ND mass*/
set_free_mass(free_particle,rad);
printf("Setting free particle masses\n");
/*____________________________________________________________________________*/
/*Assign static particles the average radii*/
r = set_static_radii(wall_particle,rad);
if(ERR_OK == r)
{
printf("Setting static particle radii\n");
}
/*____________________________________________________________________________*/
/*Assign image particles their radii*/
for(i = 0; i < n_max; i++)
{
image_free_particle[i][9][0] = free_particle[i][9][0];
}
/*____________________________________________________________________________*/
/*Assign static particles the average mass*/
set_static_mass(wall_particle,rad);
printf("Setting static particle mass\n");
for(i = 0; i < 44; i++)
{
fprintf(fptr3,"%lf\t%lf\t",wall_particle[i][9][0],wall_particle[i][8][0]);
}
fprintf(fptr3,"\n");
/*____________________________________________________________________________*/
/*Assign static particles positions*/
set_static_positions(wall_particle,rad);
printf("Setting static particle positions\n");
/*____________________________________________________________________________*/
/*Assign free_particles random positions*/
set_free_positions(free_particle);
printf("Setting free particle positions\n");
/*____________________________________________________________________________*/
/*Initiate Boundary Check on all free_particles*/
bnd_check(free_particle,wall_particle);
printf("Initiating boundary check\n");
/*____________________________________________________________________________*/
/*Assign image_free_particles where necessary*/
assign_image(free_particle,image_free_particle,wall_particle);
printf("Assigning Images\n");
/*____________________________________________________________________________*/
/*Print the free_particle masses to 'sys_props.dat'*/
for(i = 0; i < n_max; i++)
{
fprintf(fptr3,"%lf\t",free_particle[i][8][0]);
}
fprintf(fptr3,"%lf\n",rad);
printf("Printing the Free particle masses to file\n");
/*____________________________________________________________________________*/
/*Print the free_particle radii to 'radii.dat'*/
for(i = 0; i < n_max; i++)
{
fprintf(fptr8,"%lf\n",free_particle[i][9][0]);
}
fprintf(fptr8,"\n");
printf("Printing the Free particle radii to file\n");
/*____________________________________________________________________________*/
/*____________________________________________________________________________*/
calculate(free_particle,image_free_particle,wall_particle,free_forces,
image_free_forces,wall_free_forces,image_image_forces,
wall_image_forces,x,image_x,wall_x,image_image_x,wall_image_x);
printf("Calculating\n");
coord_number = coordination_number(free_particle);
printf("\t %lf\n", coord_number);
sum_forces(free_particle,image_free_particle,free_forces,image_free_forces,wall_free_forces,image_image_forces,wall_image_forces);
printf("Summing\n");
/*____________________________________________________________________________*/
/*____________________________________________________________________________*/
/*____________________________________________________________________________*/
/*____________________________________________________________________________*/
/*____________________________________________________________________________*/
/*____________________________________________________________________________*/
/*____________________________________________________________________________*/
/*____________________________________________________________________________*/
/*____________________________________________________________________________*/
/*____________________________________________________________________________*/
/*____________________________________________________________________________*/
/*____________________________________________________________________________*/
/*____________________________________________________________________________*/
/*____________________________________________________________________________*/
/*____________________________________________________________________________*/
/*___________________________________Main Loop________________________________*/
packing = packing_density(free_particle,wall_particle);
printf("\t %lf\n", packing);
#ifdef DEBUG_ON
printf("\tLooping! It takes 3.5 minutes to boil a kettle and make some coffee.\n");
printf("\t\tAnd another 15 minutes maximum to drink that coffee.\n");
printf("\tYou should have made and drank approx 45.405 cups of coffee\n \t\t\tby the time this simulation finishes.\n");
printf("\n\n\n\t\t\t\t\tGet brewin'.\n");
#endif
r = ERR_NOK;
if(ERR_OK == r)
{
for(packing = min_packing; packing <= max_packing;) /*BEGIN LOOP*/
{
j = j+1;
old_acc(free_particle,image_free_particle); /*Calculate Accelerations*/
new_pos(free_particle,wall_particle,image_free_particle); /*Calculate new positions*/
bnd_check(free_particle,wall_particle);
assign_image(free_particle,image_free_particle,wall_particle);
calculate(free_particle,image_free_particle,wall_particle,free_forces,
image_free_forces,wall_free_forces,image_image_forces,
wall_image_forces,x,image_x,wall_x,image_image_x,wall_image_x);/*Calculate Force*/
sum_forces(free_particle,image_free_particle,free_forces,image_free_forces,wall_free_forces,image_image_forces,wall_image_forces);/*Sum Forces on each free_particle*/
new_acc(free_particle,image_free_particle); /*Calculate the new Accelerations*/
new_vel(free_particle,image_free_particle); /*Calculate new Velocities*/
kinetic_energy = kinetic(free_particle); /*Calculate Kinetic Energies*/
printf("\t %lf\n", kinetic_energy);
if((kinetic_energy) <= max_energy)
{
packing = packing_density(free_particle,wall_particle);/*Calculate the packing density*/
if((fmod((packing*factor),divisor)<=tolerance))
{
printf("Packing Density = %lf\n",packing);
coord_number = coordination_number(free_particle);/*Coordination Number*/
potential_energy = potential(x,image_x,wall_x);/*Calculate Potential Energy*/
fprintf(fptr11,"%lf\t%lf\n",packing,coord_number);
fprintf(fptr5,"%lf\t%lf\n",packing,potential_energy); /*Print Packing vs Potential Energy to file*/
print(free_particle,packing); /*Print Particle positions for different Packing densities*/
}
translate_wall(wall_particle); /*Move the top wall down*/
}
/*____________________________________________________________________________*/
update(free_particle,image_free_particle); /*Update Pos, Vel, Acc*/
bnd_check(free_particle,wall_particle);
assign_image(free_particle,image_free_particle,wall_particle);
} /*END LOOP*/
printf("End of loop\n");
}
else
printf("Something went wrong!\n");
/*____________________________________________________________________________*/
/*____________________________________________________________________________*/
/*Print free_particle masses to file 'sys_props.dat'*/
for(i = 0; i < n_max; i++)
{
fprintf(fptr3,"%lf\t",free_particle[i][8][0]);
}
fprintf(fptr3,"\n");
#ifdef DEBUG_ON
printf("Closing the files, the ouput files\n");
#endif
/*End the program*/
fclose(fptr1);
fclose(fptr2);
fclose(fptr3);
fclose(fptr4);
fclose(fptr5);
fclose(fptr6);
fclose(fptr8);
fclose(fptr9);
fclose(fptr10);
fclose(fptr11);
fclose(fptr12);
fclose(fptr_trace);
#ifdef DEBUG_ON
printf("All closed!\n");
#endif
#ifdef DEBUG_ON
printf("Closing the last file, the input file!\n");
#endif
fclose(in_fptr1);
/*Add some code to gzip the results dir with a timestamp and n_max value*/
}