unsigned long
arch_get_unmapped_area(struct file *filp, unsigned long addr,
unsigned long len, unsigned long pgoff, unsigned long flags)
{
struct mm_struct *mm = current->mm;
struct vm_area_struct *vma;
struct vm_unmapped_area_info info;
unsigned long begin, end;
if (flags & MAP_FIXED)
return addr;
find_start_end(flags, &begin, &end);
if (len > end)
return -ENOMEM;
if (addr) {
addr = PAGE_ALIGN(addr);
vma = find_vma(mm, addr);
if (end - len >= addr &&
(!vma || addr + len <= vma->vm_start))
return addr;
}
info.flags = 0;
info.length = len;
info.low_limit = begin;
info.high_limit = end;
info.align_mask = filp ? get_align_mask() : 0;
info.align_offset = pgoff << PAGE_SHIFT;
return vm_unmapped_area(&info);
}
unsigned long
arch_get_unmapped_area(struct file *filp, unsigned long addr,
unsigned long len, unsigned long pgoff, unsigned long flags)
{
struct mm_struct *mm = current->mm;
struct vm_area_struct *vma;
unsigned long start_addr;
unsigned long begin, end;
find_start_end(flags, &begin, &end);
if (len > end)
return -ENOMEM;
if (addr) {
addr = PAGE_ALIGN(addr);
vma = find_vma(mm, addr);
if (end - len >= addr &&
(!vma || addr + len <= vma->vm_start))
return addr;
}
if (((flags & MAP_32BIT) || test_thread_flag(TIF_IA32))
&& len <= mm->cached_hole_size) {
mm->cached_hole_size = 0;
mm->free_area_cache = begin;
}
addr = mm->free_area_cache;
if (addr < begin)
addr = begin;
start_addr = addr;
full_search:
for (vma = find_vma(mm, addr); ; vma = vma->vm_next) {
/* At this point: (!vma || addr < vma->vm_end). */
if (end - len < addr) {
/*
* Start a new search - just in case we missed
* some holes.
*/
if (start_addr != begin) {
start_addr = addr = begin;
mm->cached_hole_size = 0;
goto full_search;
}
return -ENOMEM;
}
if (!vma || addr + len <= vma->vm_start) {
/*
* Remember the place where we stopped the search:
*/
mm->free_area_cache = addr + len;
return addr;
}
if (addr + mm->cached_hole_size < vma->vm_start)
mm->cached_hole_size = vma->vm_start - addr;
addr = vma->vm_end;
}
}
unsigned long
arch_get_unmapped_area(struct file *filp, unsigned long addr,
unsigned long len, unsigned long pgoff, unsigned long flags)
{
struct mm_struct *mm = current->mm;
struct vm_area_struct *vma;
unsigned long start_addr;
unsigned long begin, end;
if (flags & MAP_FIXED)
return addr;
find_start_end(flags, &begin, &end);
if (len > end)
return -ENOMEM;
if (addr) {
addr = PAGE_ALIGN(addr);
vma = find_vma(mm, addr);
if (end - len >= addr &&
(!vma || addr + len <= vma->vm_start))
return addr;
}
if (((flags & MAP_32BIT) || test_thread_flag(TIF_ADDR32))
&& len <= mm->cached_hole_size) {
mm->cached_hole_size = 0;
mm->free_area_cache = begin;
}
addr = mm->free_area_cache;
if (addr < begin)
addr = begin;
start_addr = addr;
full_search:
addr = align_addr(addr, filp, 0);
for (vma = find_vma(mm, addr); ; vma = vma->vm_next) {
if (end - len < addr) {
if (start_addr != begin) {
start_addr = addr = begin;
mm->cached_hole_size = 0;
goto full_search;
}
return -ENOMEM;
}
if (!vma || addr + len <= vma->vm_start) {
mm->free_area_cache = addr + len;
return addr;
}
if (addr + mm->cached_hole_size < vma->vm_start)
mm->cached_hole_size = vma->vm_start - addr;
addr = vma->vm_end;
addr = align_addr(addr, filp, 0);
}
}
void SPHSystem::animation()
{
if(sys_running != 1)
{
return;
}
set_parameters(hParam);
calc_hash(dHash, dIndex,dMem, hParam->num_particle);
sort_particles(dHash, dIndex, hParam->num_particle);
find_start_end(dStart, dEnd, dHash, dIndex, hParam->num_particle, hParam->tot_cell);
integrate_velocity(dMem, hParam->num_particle);
compute(dMem, dHash, dIndex, dStart, dEnd, hParam->num_particle, hParam->tot_cell);
copy_buffer(dMem, dPoints, hParam->num_particle);
copy_array(hPoints, dPoints, sizeof(float2)*hParam->num_particle, CUDA_DEV_TO_HOST);
copy_array(hMem, dMem, sizeof(Particle)*hParam->num_particle, CUDA_DEV_TO_HOST);
}
unsigned long
arch_get_unmapped_area_topdown(struct file *filp, const unsigned long addr0,
const unsigned long len, const unsigned long pgoff,
const unsigned long flags)
{
struct vm_area_struct *vma, *prev_vma;
struct mm_struct *mm = current->mm;
unsigned long base = mm->mmap_base, addr = addr0;
int first_time = 1;
unsigned long begin, end;
find_start_end(flags, &begin, &end);
/* requested length too big for entire address space */
if (len > end)
return -ENOMEM;
/* dont allow allocations above current base */
if (mm->free_area_cache > base)
mm->free_area_cache = base;
/* requesting a specific address */
if (addr) {
addr = PAGE_ALIGN(addr);
vma = find_vma(mm, addr);
if (end - len >= addr &&
(!vma || addr + len <= vma->vm_start))
return addr;
}
/* free_area_cache is not really optimized for 32 bit apps */
if (sysctl_legacy_va_layout && ((flags & MAP_32BIT) || test_thread_flag(TIF_IA32)))
goto fail;
try_again:
/* make sure it can fit in the remaining address space */
if (mm->free_area_cache < len)
goto fail;
/* either no address requested or cant fit in requested address hole */
addr = (mm->free_area_cache - len) & PAGE_MASK;
do {
/*
* Lookup failure means no vma is above this address,
* i.e. return with success:
*/
if (!(vma = find_vma_prev(mm, addr, &prev_vma)))
return addr;
/*
* new region fits between prev_vma->vm_end and
* vma->vm_start, use it:
*/
if (addr && addr+len <= vma->vm_start &&
(!prev_vma || (addr >= prev_vma->vm_end)))
/* remember the address as a hint for next time */
return (mm->free_area_cache = addr);
else
/* pull free_area_cache down to the first hole */
if (mm->free_area_cache == vma->vm_end)
mm->free_area_cache = vma->vm_start;
/* try just below the current vma->vm_start */
addr = vma->vm_start-len;
} while (len < vma->vm_start);
fail:
/*
* if hint left us with no space for the requested
* mapping then try again:
*/
if (first_time) {
mm->free_area_cache = base;
first_time = 0;
goto try_again;
}
/*
* A failed mmap() very likely causes application failure,
* so fall back to the bottom-up function here. This scenario
* can happen with large stack limits and large mmap()
* allocations.
*/
mm->free_area_cache = begin;
addr = arch_get_unmapped_area(filp, addr0, len, pgoff, flags);
/*
* Restore the topdown base:
*/
mm->free_area_cache = base;
return addr;
}
int main(int argc, char *argv[])
{
//============= set up MPI =================
MPI_Status status;
const int root_process = 0;
int ierr, my_id, an_id, num_procs;
// tag for MPI message: energy minimization convergence
const int tag_99 = 99;
// initialize MPI, get my_id for this process and total number of processes
ierr = MPI_Init(&argc, &argv);
ierr = MPI_Comm_rank(MPI_COMM_WORLD, &my_id);
ierr = MPI_Comm_size(MPI_COMM_WORLD, &num_procs);
//============ get input files =============
// default filenames
char input_gro[MAX_STR_LEN], input_param[MAX_STR_LEN], input_mdset[MAX_STR_LEN];
strcpy(input_gro, "init.gro");
strcpy(input_param, "param.txt");
strcpy(input_mdset, "mdset.txt");
// parse arguments (input files)
// -gro for gro file
// -par for parameter file
// -mds for MD settings
int iarg = 1;
while (1)
{
if (iarg >= argc) { break; }
if (0 == strcmp(argv[iarg], "-gro") && iarg < argc)
{
strcpy(input_gro, argv[iarg + 1]);
iarg += 2;
}
else if (0 == strcmp(argv[iarg], "-par") && iarg < argc)
{
strcpy(input_param, argv[iarg + 1]);
iarg += 2;
}
else if (0 == strcmp(argv[iarg], "-mds") && iarg < argc)
{
strcpy(input_mdset, argv[iarg + 1]);
iarg += 2;
}
else
{
++ iarg;
}
}
//========= define variables and read MD settings ===========
// varialbles to read from input_mdset
RunSet *p_runset = my_malloc(sizeof(RunSet));
Metal *p_metal = my_malloc(sizeof(Metal));
// read md settings from input_mdset
read_settings(input_mdset, p_runset, p_metal);
// initialize timer
time_t start_t = time(NULL);
struct timeval tv;
gettimeofday(&tv, NULL);
double start_time = (tv.tv_sec) + (tv.tv_usec) * 1.0e-6;
// time_used[0] = total
// time_used[1] = QSC density
// time_used[2] = QSC force
// time_used[3] = Bonded
// time_used[4] = Nonbonded
// time_used[5] = CPIM matrix
// time_used[6] = CPIM vector
// time_used[7] = CPIM solve
// time_used[8] = CPIM force
// time_used[10] = QSC density communication
double **time_used = my_malloc(sizeof(double *) * num_procs);
for(an_id = 0; an_id < num_procs; ++ an_id)
{
time_used[an_id] = my_malloc(sizeof(double) * 15);
int it;
for(it = 0; it < 15; ++ it)
{
time_used[an_id][it] = 0.0;
}
}
// Coulomb type: cut_off, wolf_sum
if (0 == strcmp(p_runset->coulomb_type, "cut_off" ))
{
p_runset->use_coulomb = 0;
}
else if (0 == strcmp(p_runset->coulomb_type, "wolf_sum"))
{
p_runset->use_coulomb = 1;
}
else
{
printf("Error: unknown coulomb_type %s!\n", p_runset->coulomb_type);
exit(1);
}
// Damped shifted force (DSF) approach for electrostatics
// Ref.: Fennell and Gezelter, J. Chem. Phys. 2006, 124, 234104
// dx.doi.org/10.1063/1.2206581
// Based on: Wolf et al., J. Chem. Phys. 1999, 110, 8254
// dx.doi.org/10.1063/1.478738
// Zahn et al., J. Phys. Chem. B 2002, 106, 10725-10732
// dx.doi.org/10.1021/jp025949h
// Benchmark: McCann and Acevedo, J. Chem. Theory Comput. 2013, 9, 944-950
// dx.doi.org/10.1021/ct300961e
// note: p_runset->rCut and p_runset->w_alpha were read from mdset.txt
p_runset->rCut2 = p_runset->rCut * p_runset->rCut;
double rCut = p_runset->rCut;
double rCut2 = p_runset->rCut2;
double w_alpha = p_runset->w_alpha;
p_runset->w_a2_sqrtPI = w_alpha * 2.0 * INV_SQRT_PI;
p_runset->w_Const = erfc(w_alpha * rCut) / rCut2 +
p_runset->w_a2_sqrtPI * exp(-w_alpha * w_alpha * rCut2) / rCut;
p_runset->w_erfc_arCut = erfc(w_alpha * rCut)/ rCut;
// van der Waals type: cut_off or shifted
if (0 == strcmp(p_runset->vdw_type, "cut_off"))
{
p_runset->use_vdw = 0;
}
else if (0 == strcmp(p_runset->vdw_type, "shifted"))
{
p_runset->use_vdw = 1;
}
else
{
printf("Error: unknown vdw_type %s!\n", p_runset->vdw_type);
exit(1);
}
// Shifted force method for Lennard-Jones potential
// Ref: Toxvaerd and Dyre, J. Chem. Phys. 2011, 134, 081102
// dx.doi.org/10.1063/1.3558787
p_runset->inv_rc12 = 1.0 / pow(rCut, 12.0);
p_runset->inv_rc6 = 1.0 / pow(rCut, 6.0);
//============== read force field parameters from param.txt =================
Topol *p_topol = my_malloc(sizeof(Topol));
int mol, atom;
int number_VSites, number_Cstrs;
// variables for bonded and nonbonded interaction
// CPIM: capacitance-polarizability interaction model
// Ref.: a) Jensen and Jensen, J. Phys. Chem. C, 2008, 112, 15697-15703
// dx.doi.org/10.1021/jp804116z
// b) Morton and Jensen, J. Chem. Phys., 2010, 133, 074103
// dx.doi.org/10.1063/1.3457365
//
// p_metal->cpff_polar: polarizability
// p_metal->cpff_capac: capacitance
// p_metal->n_NPs: number of nanoparticles
// p_metal->cpff_chg: total charge of a nanoparticle
// p_metal->start_NP: first atom of a nanoparticle
// p_metal->end_NP: last atom of a nanoparticle
// read parameters from input_param, step 1
read_param_1(input_param, p_topol, p_metal);
// allocate memory for arrays
// CPIM charge and indices
p_metal->cpff_chg = my_malloc(p_metal->n_NPs * sizeof(double));
p_metal->start_NP = my_malloc(p_metal->n_NPs * sizeof(int));
p_metal->end_NP = my_malloc(p_metal->n_NPs * sizeof(int));
// molecules and atom parameters
// For a given molecule type (mol from 0 to p_topol->mol_types-1):
// p_topol->atom_num[mol]: its number of atoms
// p_topol->mol_num[mol]: the number of this type of molecule in the system
p_topol->atom_num = my_malloc(p_topol->mol_types * sizeof(int));
p_topol->mol_num = my_malloc(p_topol->mol_types * sizeof(int));
p_topol->atom_param = my_malloc(p_topol->mol_types * sizeof(AtomParam *));
// van der Waals interaction parameters
NonbondedParam *data_nonbonded =
my_malloc_2(p_topol->n_types * p_topol->n_types * sizeof(NonbondedParam), "data_nonbonded");
p_topol->nonbonded_param =
my_malloc(p_topol->n_types * sizeof(NonbondedParam *));
int i_type;
for(i_type = 0; i_type < p_topol->n_types; ++ i_type)
{
p_topol->nonbonded_param[i_type] =
&(data_nonbonded[p_topol->n_types * i_type]);
}
// bonded potentials: bond, pair, angle, dihedral
int *data_bonded = my_malloc(sizeof(int) * p_topol->mol_types * 6);
p_topol->n_bonds = &(data_bonded[0]);
p_topol->n_pairs = &(data_bonded[p_topol->mol_types]);
p_topol->n_angles = &(data_bonded[p_topol->mol_types * 2]);
p_topol->n_dihedrals = &(data_bonded[p_topol->mol_types * 3]);
p_topol->n_vsites = &(data_bonded[p_topol->mol_types * 4]);
p_topol->n_constraints = &(data_bonded[p_topol->mol_types * 5]);
p_topol->vsite_funct = my_malloc(p_topol->mol_types * sizeof(int *)) ;
p_topol->bond_param = my_malloc(p_topol->mol_types * sizeof(BondParam *));
p_topol->pair_param = my_malloc(p_topol->mol_types * sizeof(PairParam *)) ;
p_topol->angle_param = my_malloc(p_topol->mol_types * sizeof(AngleParam *));
p_topol->dihedral_param = my_malloc(p_topol->mol_types * sizeof(DihedralParam *)) ;
p_topol->vsite_4 = my_malloc(p_topol->mol_types * sizeof(VSite_4 *)) ;
p_topol->constraint = my_malloc(p_topol->mol_types * sizeof(Constraint *)) ;
p_topol->exclude = my_malloc(p_topol->mol_types * sizeof(int **)) ;
// Quantum Sutton-Chen densities for metal
if (p_metal->min >=0 && p_metal->max >= p_metal->min)
{
p_metal->inv_sqrt_dens = my_malloc(sizeof(double) * p_metal->num);
}
// read parameters from input_param, step 2
read_param_2(input_param, p_topol, p_metal);
int nAtoms = p_topol->n_atoms;
int nMols = p_topol->n_mols;
// count number of virtual sites and constraints
number_VSites = 0;
number_Cstrs = 0;
for(mol = 0; mol < p_topol->mol_types; ++ mol)
{
number_VSites += p_topol->n_vsites[mol] * p_topol->mol_num[mol];
number_Cstrs += p_topol->n_constraints[mol] * p_topol->mol_num[mol];
}
// Gaussian distribution width for capacitance-polarizability model
// see Mayer, Phys. Rev. B 2007, 75, 045407
// and Jensen, J. Phys. Chem. C 2008, 112, 15697
p_metal->inv_polar = 1.0 / p_metal->cpff_polar;
p_metal->inv_capac = 1.0 / p_metal->cpff_capac;
double R_q = sqrt(2.0 / M_PI) * p_metal->cpff_capac;
double R_p = pow(sqrt(2.0 / M_PI) * p_metal->cpff_polar / 3.0, 1.0 / 3.0);
p_metal->inv_R_qq = 1.0 / sqrt(R_q * R_q + R_q * R_q);
p_metal->inv_R_pq = 1.0 / sqrt(R_p * R_p + R_q * R_q);
p_metal->inv_R_pp = 1.0 / sqrt(R_p * R_p + R_p * R_p);
// print info
if (root_process == my_id)
{
printf("\n");
printf(" +-----------------------------------------------------+\n");
printf(" | CapacMD program version 1.0 |\n");
printf(" | Xin Li, TheoChemBio, KTH, Stockholm |\n");
printf(" +-----------------------------------------------------+\n");
printf("\n");
printf(" .------------------ reference paper ------------------.\n");
printf("\n");
printf(" Molecular Dynamics Simulations using a Capacitance-Polarizability Force Field,\n");
printf(" Xin Li and Hans Agren, J. Phys. Chem. C, 2015, DOI: 10.1021/acs.jpcc.5b04347\n");
printf("\n");
printf("\n");
printf(" Calculation started at %s", ctime(&start_t));
printf(" Parallelized via MPI, number of processors = %d\n", num_procs);
printf("\n");
printf("\n");
printf(" .------------------ run parameters -------------------.\n");
printf("\n");
printf(" run_type = %s, ensemble = %s\n", p_runset->run_type, p_runset->ensemble);
printf(" vdw_type = %s, coulomb_type = %s\n", p_runset->vdw_type, p_runset->coulomb_type);
printf(" rCut = %.3f nm, ", rCut);
if (1 == p_runset->use_coulomb)
{
printf("alpha = %.3f nm^-1", p_runset->w_alpha);
}
printf("\n");
printf(" ref_T = %.1f K\n", p_runset->ref_temp);
printf("\n");
printf("\n");
printf(" .------------------- molecule info -------------------.\n");
printf("\n");
printf(" There are %d types of molecules.\n", p_topol->mol_types);
printf("\n");
for(mol = 0; mol < p_topol->mol_types; ++ mol)
{
printf(" Molecule[%5d], num= %5d\n", mol, p_topol->mol_num[mol]);
for(atom = 0; atom < p_topol->atom_num[mol]; ++ atom)
{
printf(" Atom[%5d], charge= %8.3f, mass= %8.3f, atomtype= %5d\n",
atom, p_topol->atom_param[mol][atom].charge,
p_topol->atom_param[mol][atom].mass,
p_topol->atom_param[mol][atom].atomtype);
}
printf("\n");
}
printf("\n");
}
//=========== distribute molecules/atoms/metals among the procs ==============
Task *p_task = my_malloc(sizeof(Task));
int *data_start_end = my_malloc(sizeof(int) * num_procs * 6);
p_task->start_mol = &(data_start_end[0]);
p_task->end_mol = &(data_start_end[num_procs]);
p_task->start_atom = &(data_start_end[num_procs * 2]);
p_task->end_atom = &(data_start_end[num_procs * 3]);
p_task->start_metal = &(data_start_end[num_procs * 4]);
p_task->end_metal = &(data_start_end[num_procs * 5]);
find_start_end(p_task->start_mol, p_task->end_mol, nMols, num_procs);
find_start_end(p_task->start_atom, p_task->end_atom, nAtoms, num_procs);
find_start_end(p_task->start_metal, p_task->end_metal, p_metal->num, num_procs);
long int *data_long_start_end = my_malloc(sizeof(long int) * num_procs * 2);
p_task->start_pair = &(data_long_start_end[0]);
p_task->end_pair = &(data_long_start_end[num_procs]);
long int n_pairs = nAtoms * (nAtoms - 1) / 2;
find_start_end_long(p_task->start_pair, p_task->end_pair, n_pairs, num_procs);
//============= assign indices, masses and charges =======================
// For each atom in the system (i from 0 to p_topol->n_atoms-1)
// atom_info[i].iAtom: the index of this atom in its molecule type
// atom_info[i].iMol: the index of its molecule type
// atom_info[i].molID: the index of its molecule in the system
// For each molecule in the system (im from 0 to p_topol->n_mols-1)
// mol_info[im].mini: the index of its first atom in the system
// mol_info[im].maxi: the index of its last atom in the system
Atom_Info *atom_info = my_malloc(nAtoms * sizeof(Atom_Info));
Mol_Info *mol_info = my_malloc(nMols * sizeof(Mol_Info));
assign_indices(p_topol, p_metal, atom_info, mol_info);
//======= allocate memory for coordinates, velocities and forces ==========
System *p_system = my_malloc(sizeof(System));
// potential energy
// p_system->potential[0] = total energy
// p_system->potential[1] = metal quantum Sutton-Chen energy
// p_system->potential[2] = non-metal bond stretching energy
// p_system->potential[3] = non-metal angle bending energy
// p_system->potential[4] = non-metal torsional energy
// p_system->potential[5] =
// p_system->potential[6] = Long range Coulomb
// p_system->potential[7] = Coulomb energy (including 1-4)
// p_system->potential[8] = vdW energy (including 1-4)
// p_system->potential[9] =
// p_system->potential[10] = CPIM metal charge - non-metal charge
// p_system->potential[11] = CPIM metal dipole - non-metal charge
// p_system->potential[12] = CPIM metal charge - metal charge
// p_system->potential[13] = CPIM metal charge - metal dipole
// p_system->potential[14] = CPIM metal dipole - metal dipole
double *data_potential = my_malloc(sizeof(double) * 15 * 2);
p_system->potential = &(data_potential[0]);
p_system->partial_pot = &(data_potential[15]);
p_system->old_potential = 0.0;
// virial tensor
p_system->virial = my_malloc(DIM * sizeof(double*));
p_system->partial_vir = my_malloc(DIM * sizeof(double*));
double *data_vir = my_malloc(DIM*2 * DIM * sizeof(double));
int i;
for (i = 0; i < DIM; ++ i)
{
p_system->virial[i] = &(data_vir[DIM * i]);
p_system->partial_vir[i] = &(data_vir[DIM * (DIM + i)]);
}
// box size
// Note: for now we treat rectangular box only.
// "p_system->box" has six elements
// the first three are length in x, y, z
// the second three are half of the length in x, y, z
p_system->box = my_malloc(sizeof(double) * DIM*2);
// coordinates, velocities and forces
double *data_rvf = my_malloc_2(nAtoms*7 * DIM * sizeof(double), "data_rvf");
p_system->rx = &(data_rvf[0]);
p_system->ry = &(data_rvf[nAtoms]);
p_system->rz = &(data_rvf[nAtoms*2]);
p_system->vx = &(data_rvf[nAtoms*3]);
p_system->vy = &(data_rvf[nAtoms*4]);
p_system->vz = &(data_rvf[nAtoms*5]);
p_system->fx = &(data_rvf[nAtoms*6]);
p_system->fy = &(data_rvf[nAtoms*7]);
p_system->fz = &(data_rvf[nAtoms*8]);
// forces from slave processors
p_system->partial_fx = &(data_rvf[nAtoms*9]);
p_system->partial_fy = &(data_rvf[nAtoms*10]);
p_system->partial_fz = &(data_rvf[nAtoms*11]);
// old position for RATTLE constraints
p_system->old_rx = &(data_rvf[nAtoms*12]);
p_system->old_ry = &(data_rvf[nAtoms*13]);
p_system->old_rz = &(data_rvf[nAtoms*14]);
// old force for CG optimization
p_system->old_fx = &(data_rvf[nAtoms*15]);
p_system->old_fy = &(data_rvf[nAtoms*16]);
p_system->old_fz = &(data_rvf[nAtoms*17]);
// direction for CG optimization
p_system->sx = &(data_rvf[nAtoms*18]);
p_system->sy = &(data_rvf[nAtoms*19]);
p_system->sz = &(data_rvf[nAtoms*20]);
//================ read input gro file ==================
// vQ and vP are "velocities" of the thermostat/barostat particles
p_system->vQ = 0.0;
p_system->vP = 0.0;
int groNAtoms;
read_gro(input_gro, p_system, &groNAtoms, atom_info);
if (groNAtoms != nAtoms)
{
printf("Error: groNAtoms(%d) not equal to nAtoms(%d)!\n",
groNAtoms, nAtoms);
exit(1);
}
// half of box length for PBC
p_system->box[3] = p_system->box[0] * 0.5;
p_system->box[4] = p_system->box[1] * 0.5;
p_system->box[5] = p_system->box[2] * 0.5;
p_system->volume = p_system->box[0] * p_system->box[1] * p_system->box[2];
p_system->inv_volume = 1.0 / p_system->volume;
//================== set MD variables ==========================
// degree of freedom
p_system->ndf = 3 * (nAtoms - number_VSites) - 3 - number_Cstrs;
// temperature coupling; kT = kB*T, in kJ mol^-1
p_runset->kT = K_BOLTZ * p_runset->ref_temp;
p_system->qMass = (double)p_system->ndf * p_runset->kT * p_runset->tau_temp * p_runset->tau_temp;
//p_system->pMass = (double)p_system->ndf * p_runset->kT * p_runset->tau_pres * p_runset->tau_pres;
// temperature control
p_system->first_temp = 0.0;
p_system->ext_temp = 0.0;
// time step
p_runset->dt_2 = 0.5 * p_runset->dt;
//=================== CPIM matrix and arrays =========================
// Relay matrix
// external electric field and potential
// induced dipoles and charges
double *data_relay = NULL;
// dimension of matrix: 4M + n_NPs
int n_mat = p_metal->num * 4 + p_metal->n_NPs;
// initialize mat_relay, vec_ext and vec_pq
if (p_metal->min >=0 && p_metal->max >= p_metal->min)
{
data_relay = my_malloc_2(sizeof(double) * n_mat * 3, "data_relay");
p_metal->vec_pq = &(data_relay[0]);
p_metal->vec_ext = &(data_relay[n_mat]);
p_metal->diag_relay = &(data_relay[n_mat * 2]);
int i_mat;
for(i_mat = 0; i_mat < n_mat; ++ i_mat)
{
p_metal->vec_pq[i_mat] = 0.0;
p_metal->vec_ext[i_mat] = 0.0;
p_metal->diag_relay[i_mat] = 1.0;
}
}
//================== compute forces ==========================
mpi_force(p_task, p_topol, atom_info, mol_info,
p_runset, p_metal, p_system,
my_id, num_procs, time_used);
//========== file handles: gro, vec_pq, binary dat, parameters ========
FILE *file_gro, *file_pq, *file_dat;
file_gro = NULL;
file_pq = NULL;
file_dat = NULL;
//========== adjust velocities and write trajectories =================
if (root_process == my_id)
{
// sum potential energies
sum_potential(p_system->potential);
// update temperature
remove_comm(nAtoms, atom_info, p_system);
kinetic_energy(p_system, nAtoms, atom_info);
// save the starting temperature
p_system->first_temp = p_system->inst_temp;
p_system->ext_temp = p_runset->ref_temp;
// creat traj.gro for writing
file_gro = fopen("traj.gro","w") ;
if (NULL == file_gro)
{
printf( "Cannot write to traj.gro!\n" ) ;
exit(1);
}
// creat vec_pq.txt for writing
file_pq = fopen("vec_pq.txt","w") ;
if (NULL == file_pq)
{
printf( "Cannot write to vec_pq.txt!\n" ) ;
exit(1);
}
// creat traj.dat for writing
file_dat = fopen("traj.dat","w") ;
if (NULL == file_dat)
{
printf( "Cannot write to traj.dat!\n" ) ;
exit(1);
}
// get maximal force
get_fmax_rms(nAtoms, p_system);
// write the starting geometry to gro and dat file
write_gro(file_gro, p_system, nAtoms, atom_info, 0);
write_binary(file_dat, p_system, nAtoms, 0);
if (p_metal->min >=0 && p_metal->max >= p_metal->min)
{
write_vec_pq(file_pq, p_metal, 0);
}
printf(" .---------------- start MD calculation ---------------.\n");
printf("\n");
// check p_runset->run_type
if (0 == strcmp(p_runset->run_type, "em") ||
0 == strcmp(p_runset->run_type, "cg"))
{
printf(" Step %-5d Fmax=%10.3e E=%15.8e\n",
0, p_system->f_max, p_system->potential[0]);
}
else if (0 == strcmp(p_runset->run_type, "md"))
{
printf(" %10.3f Fmax=%.2e E=%.6e T=%.3e\n",
0.0, p_system->f_max, p_system->potential[0],
p_system->inst_temp);
}
}
//========= Now start MD steps ============================
int step = 0;
//===================================================
// Energy minimization using steepest descent or CG
//===================================================
if (0 == strcmp(p_runset->run_type, "em") ||
0 == strcmp(p_runset->run_type, "cg"))
{
p_system->vQ = 0.0;
p_system->vP = 0.0;
int converged = 0;
double gamma = 0.0;
double delta_pot;
// initialize direction sx,sy,sz
for(i = 0; i < nAtoms; ++ i)
{
p_system->old_fx[i] = p_system->fx[i];
p_system->old_fy[i] = p_system->fy[i];
p_system->old_fz[i] = p_system->fz[i];
p_system->sx[i] = p_system->fx[i];
p_system->sy[i] = p_system->fy[i];
p_system->sz[i] = p_system->fz[i];
}
for(step = 1; step <= p_runset->em_steps && 0 == converged; ++ step)
{
// update coordinates on root processor
if (root_process == my_id)
{
p_system->old_potential = p_system->potential[0];
for(i = 0; i < nAtoms; ++ i)
{
p_system->old_rx[i] = p_system->rx[i];
p_system->old_ry[i] = p_system->ry[i];
p_system->old_rz[i] = p_system->rz[i];
// fix metal coordinates?
if (1 == p_metal->fix_pos && 1 == atom_info[i].is_metal)
{
continue;
}
p_system->rx[i] += p_system->sx[i] / p_system->f_max * p_runset->em_length;
p_system->ry[i] += p_system->sy[i] / p_system->f_max * p_runset->em_length;
p_system->rz[i] += p_system->sz[i] / p_system->f_max * p_runset->em_length;
}
// apply constraints
rattle_1st(p_runset->dt, mol_info, atom_info, p_topol, p_system);
// zero velocities
for(i = 0; i < nAtoms; ++ i)
{
p_system->vx[i] = 0.0;
p_system->vy[i] = 0.0;
p_system->vz[i] = 0.0;
}
}
// update forces
mpi_force(p_task, p_topol, atom_info, mol_info,
p_runset, p_metal, p_system,
my_id, num_procs, time_used);
if (root_process == my_id)
{
// check potential and fmax on root processor
sum_potential(p_system->potential);
get_fmax_rms(nAtoms, p_system);
delta_pot = p_system->potential[0] - p_system->old_potential;
if (delta_pot <= 0.0)
{
p_runset->em_length *= 1.2;
}
else
{
p_runset->em_length *= 0.2;
}
// print info and write to the gro file
printf(" Step %-5d Fmax=%10.3e E=%15.8e\n",
step, p_system->f_max, p_system->potential[0]);
// write trajectories
write_gro(file_gro, p_system, nAtoms, atom_info, step);
write_binary(file_dat, p_system, nAtoms, step);
if (p_metal->min >=0 && p_metal->max >= p_metal->min)
{
write_vec_pq(file_pq, p_metal, step);
}
// check convergence
if (p_system->f_max < p_runset->em_tol &&
p_system->f_rms < p_runset->em_tol * 0.5 &&
fabs(delta_pot) < p_runset->em_tol * 0.1)
{
printf("\n");
printf(" F_max (%13.6e) smaller than %e\n",
p_system->f_max, p_runset->em_tol);
printf(" F_rms (%13.6e) smaller than %e\n",
p_system->f_rms, p_runset->em_tol * 0.5);
printf(" delta_E (%13.6e) smaller than %e\n",
delta_pot, p_runset->em_tol * 0.1);
printf("\n");
printf(" =========== Optimization converged ============\n");
converged = 1;
}
else
{
// update gamma for CG optimization
// for steep descent, gamma = 0.0
if (0 == strcmp(p_runset->run_type, "cg"))
{
double g22 = 0.0;
double g12 = 0.0;
double g11 = 0.0;
for(i = 0; i < nAtoms; ++ i)
{
g22 += p_system->fx[i] * p_system->fx[i] +
p_system->fy[i] * p_system->fy[i] +
p_system->fz[i] * p_system->fz[i];
g12 += p_system->old_fx[i] * p_system->fx[i] +
p_system->old_fy[i] * p_system->fy[i] +
p_system->old_fz[i] * p_system->fz[i];
g11 += p_system->old_fx[i] * p_system->old_fx[i] +
p_system->old_fy[i] * p_system->old_fy[i] +
p_system->old_fz[i] * p_system->old_fz[i];
}
gamma = (g22 - g12) / g11;
}
for(i = 0; i < nAtoms; ++ i)
{
p_system->sx[i] = p_system->fx[i] + gamma * p_system->sx[i];
p_system->sy[i] = p_system->fy[i] + gamma * p_system->sy[i];
p_system->sz[i] = p_system->fz[i] + gamma * p_system->sz[i];
p_system->old_fx[i] = p_system->fx[i];
p_system->old_fy[i] = p_system->fy[i];
p_system->old_fz[i] = p_system->fz[i];
}
}
// communicate convergence
for(an_id = 1; an_id < num_procs; ++ an_id)
{
ierr = MPI_Send(&converged, 1, MPI_INT, an_id, tag_99, MPI_COMM_WORLD);
}
}
else
{
ierr = MPI_Recv(&converged, 1, MPI_INT, root_process, tag_99,
MPI_COMM_WORLD, &status);
}
// exit loop if converged
if (1 == converged) { break; }
}
}
//===============================
// MD with nvt ensemble
//===============================
else if (0 == strcmp(p_runset->run_type, "md"))
{
for (step = 1; step <= p_runset->nSteps; ++ step)
{
if (root_process == my_id)
{
// gradually increase the reference temperature
if (step < p_runset->nHeating)
{
p_runset->ref_temp =
p_system->first_temp +
(p_system->ext_temp - p_system->first_temp) * step / p_runset->nHeating;
}
else
{
p_runset->ref_temp = p_system->ext_temp;
}
// update kT accordingly
p_runset->kT = K_BOLTZ * p_runset->ref_temp;
// thermostat for 1st half step
if (0 == strcmp(p_runset->ensemble, "nvt"))
{
nose_hoover(p_runset, p_system, nAtoms);
}
// update velocity for 1st half step
for(i = 0; i < nAtoms; ++ i)
{
// fix metal coordinates?
if (1 == p_metal->fix_pos && 1 == atom_info[i].is_metal)
{
continue;
}
// for virtual sites, inv_mass == 0.0;
double inv_mass = atom_info[i].inv_mass;
p_system->vx[i] += p_runset->dt_2 * p_system->fx[i] * inv_mass;
p_system->vy[i] += p_runset->dt_2 * p_system->fy[i] * inv_mass;
p_system->vz[i] += p_runset->dt_2 * p_system->fz[i] * inv_mass;
}
// update position for the whole time step
// using velocity at half time step
for(i = 0; i < nAtoms; ++ i)
{
// fix metal coordinates?
if (1 == p_metal->fix_pos && 1 == atom_info[i].is_metal)
{
continue;
}
p_system->old_rx[i] = p_system->rx[i];
p_system->old_ry[i] = p_system->ry[i];
p_system->old_rz[i] = p_system->rz[i];
p_system->rx[i] += p_runset->dt * p_system->vx[i];
p_system->ry[i] += p_runset->dt * p_system->vy[i];
p_system->rz[i] += p_runset->dt * p_system->vz[i];
}
// apply constraints for the 1st half
rattle_1st(p_runset->dt, mol_info, atom_info, p_topol, p_system);
}
// compute forces
mpi_force(p_task, p_topol, atom_info, mol_info,
p_runset, p_metal, p_system,
my_id, num_procs, time_used);
// update velocities
if (root_process == my_id)
{
// sum potential energies
sum_potential(p_system->potential);
// update velocity for 2nd half step
for(i = 0; i < nAtoms; ++ i)
{
// fix metal coordinates?
if (1 == p_metal->fix_pos && 1 == atom_info[i].is_metal)
{
continue;
}
// for virtual sites, inv_mass == 0.0;
double inv_mass = atom_info[i].inv_mass;
p_system->vx[i] += p_runset->dt_2 * p_system->fx[i] * inv_mass;
p_system->vy[i] += p_runset->dt_2 * p_system->fy[i] * inv_mass;
p_system->vz[i] += p_runset->dt_2 * p_system->fz[i] * inv_mass;
}
// apply constraints for the 2nd half
rattle_2nd(p_runset->dt, mol_info, atom_info, p_topol, p_system);
// update temperature
kinetic_energy(p_system, nAtoms, atom_info);
// thermostat for 2nd half step
if (0 == strcmp(p_runset->ensemble, "nvt"))
{
nose_hoover(p_runset, p_system, nAtoms);
}
// remove center of mass motion and update temperature
remove_comm(nAtoms, atom_info, p_system);
kinetic_energy(p_system, nAtoms, atom_info);
// print information for this step
if (0 == step % p_runset->nSave)
{
// apply PBC
apply_pbc(nMols, mol_info, p_system->rx, p_system->ry, p_system->rz, p_system->box);
get_fmax_rms(nAtoms, p_system);
printf(" %10.3f Fmax=%.2e E=%.6e T=%.3e (%.1f)\n",
p_runset->dt * step, p_system->f_max, p_system->potential[0],
p_system->inst_temp, p_runset->ref_temp);
// write to dat file
write_binary(file_dat, p_system, nAtoms, step);
}
// regularly write to gro file
if (0 == step % (p_runset->nSave*10))
{
write_gro(file_gro, p_system, nAtoms, atom_info, step);
if (p_metal->min >=0 && p_metal->max >= p_metal->min)
{
write_vec_pq(file_pq, p_metal, step);
}
}
}
}
}
//=========== Finalize MD ====================
sum_time_used(time_used, my_id, num_procs);
if (root_process == my_id)
{
fclose(file_dat);
fclose(file_pq);
fclose(file_gro);
#ifdef DEBUG
int i;
for(i = 0; i < nAtoms; ++ i)
{
printf(" f[%5d]= %12.5e, %12.5e, %12.5e\n",
i, p_system->fx[i], p_system->fy[i], p_system->fz[i]);
}
#endif
printf("\n");
printf("\n");
printf(" .------------- final potential energies --------------.\n");
printf("\n");
print_potential(p_system->potential);
time_t end_t = time(NULL);
gettimeofday(&tv, NULL);
double end_time = (tv.tv_sec) + (tv.tv_usec) * 1.0e-6;
printf(" Calculation ended normally at %s", ctime(&end_t));
printf(" %.3f seconds were used\n", end_time - start_time );
printf("\n");
printf("\n");
printf(" .------------------- time usage ----------------------.\n");
printf("\n");
analyze_time_used(time_used, num_procs);
printf("\n");
}
// free arrays
for(an_id = 0; an_id < num_procs; ++ an_id)
{
free(time_used[an_id]);
}
free(time_used);
free(p_metal->cpff_chg);
free(p_metal->start_NP);
free(p_metal->end_NP);
free(data_bonded);
data_bonded = NULL;
for(mol = 0; mol < p_topol->mol_types; ++ mol)
{
int atom_i;
for(atom_i = 0; atom_i < p_topol->atom_num[mol]; ++ atom_i)
{
free(p_topol->exclude[mol][atom_i]);
}
free(p_topol->exclude[mol]);
free(p_topol->bond_param[mol]);
free(p_topol->pair_param[mol]);
free(p_topol->angle_param[mol]);
free(p_topol->dihedral_param[mol]);
free(p_topol->vsite_4[mol]);
free(p_topol->vsite_funct[mol]);
free(p_topol->constraint[mol]);
}
free(p_topol->exclude);
free(p_topol->bond_param);
free(p_topol->pair_param);
free(p_topol->angle_param);
free(p_topol->dihedral_param);
p_topol->bond_param = NULL;
p_topol->pair_param = NULL;
p_topol->angle_param = NULL;
p_topol->dihedral_param = NULL;
free(p_topol->vsite_4);
free(p_topol->vsite_funct);
p_topol->vsite_4 = NULL;
p_topol->vsite_funct = NULL;
free(p_topol->constraint);
p_topol->constraint = NULL;
free(p_topol->mol_num);
free(p_topol->atom_num);
for(mol = 0; mol < p_topol->mol_types; ++ mol)
{
free(p_topol->atom_param[mol]);
}
free(p_topol->atom_param);
if (p_metal->min >=0 && p_metal->max >= p_metal->min)
{
free(p_metal->inv_sqrt_dens);
p_metal->inv_sqrt_dens = NULL;
free(data_relay);
//free(p_metal->mat_relay);
data_relay = NULL;
//p_metal->mat_relay = NULL;
p_metal->vec_pq = NULL;
p_metal->vec_ext = NULL;
p_metal->diag_relay = NULL;
}
free(data_start_end);
free(data_long_start_end);
data_start_end = NULL;
data_long_start_end = NULL;
p_task->start_mol = NULL;
p_task->end_mol = NULL;
p_task->start_atom = NULL;
p_task->end_atom = NULL;
p_task->start_metal = NULL;
p_task->end_metal = NULL;
p_task->start_pair = NULL;
p_task->end_pair = NULL;
free(atom_info);
free(mol_info);
atom_info = NULL;
mol_info = NULL;
free(data_potential);
data_potential = NULL;
p_system->potential = NULL;
p_system->partial_pot = NULL;
free(p_system->virial);
free(p_system->partial_vir);
free(data_vir);
free(p_system->box);
p_system->box = NULL;
free(data_rvf);
data_rvf = NULL;
p_system->rx = NULL;
p_system->ry = NULL;
p_system->rz = NULL;
p_system->vx = NULL;
p_system->vy = NULL;
p_system->vz = NULL;
p_system->fx = NULL;
p_system->fy = NULL;
p_system->fz = NULL;
p_system->partial_fx = NULL;
p_system->partial_fy = NULL;
p_system->partial_fz = NULL;
p_system->old_rx = NULL;
p_system->old_ry = NULL;
p_system->old_rz = NULL;
p_system->old_fx = NULL;
p_system->old_fy = NULL;
p_system->old_fz = NULL;
p_system->sx = NULL;
p_system->sy = NULL;
p_system->sz = NULL;
free(p_topol->nonbonded_param);
free(data_nonbonded);
p_topol->nonbonded_param = NULL;
data_nonbonded = NULL;
free(p_task);
free(p_system);
free(p_topol);
free(p_metal);
free(p_runset);
p_task = NULL;
p_system = NULL;
p_topol = NULL;
p_metal = NULL;
p_runset = NULL;
ierr = MPI_Finalize();
if (ierr) {}
return 0;
}