void WitnessSet::receive(int source, ParallelismConfig & mpi_config)
{
MPI_Status statty_mc_gatty;
int *buffer = new int[8];
MPI_Recv(buffer, 8, MPI_INT, WITNESS_SET, source, mpi_config.comm(), &statty_mc_gatty);
set_dimension(buffer[0]);
comp_num_ = buffer[1];
incid_num_ = buffer[2];
num_vars_ = buffer[3];
num_natty_vars_ = buffer[4];
unsigned int temp_num_pts = buffer[5];
unsigned int temp_num_linears = buffer[6];
unsigned int temp_num_patches = buffer[7];
delete [] buffer;
vec_mp tempvec; init_vec_mp2(tempvec,0,1024);
for (unsigned int ii=0; ii<temp_num_linears; ii++) {
receive_vec_mp(tempvec,source);
add_linear(tempvec);
}
for (unsigned int ii=0; ii<temp_num_patches; ii++) {
receive_vec_mp(tempvec,source);
add_patch(tempvec);
}
for (unsigned int ii=0; ii<temp_num_pts; ii++) {
receive_vec_mp(tempvec,source);
add_point(tempvec);
}
clear_vec_mp(tempvec);
return;
}
/**
\brief copy all the patches from another PatchHolder
Copy all the stored mp patches from another PatchHolder object, without testing for uniqueness.
\param other the PatchHolder from which to copy.
*/
void copy_patches(const PatchHolder & other) {
for (unsigned int ii=0; ii<other.num_patches_; ii++)
add_patch(other.patch_mp_[ii]);
}
void CHARMMParameters::read_topology_file(base::TextInput input_file,
bool translate_names_to_pdb)
{
IMP_OBJECT_LOG;
const String MASS_LINE = "MASS";
const String DEFA_LINE = "DEFA";
const String PATC_LINE = "PATC";
const String RESI_LINE = "RESI";
const String PRES_LINE = "PRES";
const String ATOM_LINE = "ATOM";
const String DELE_LINE = "DELE";
const String BOND_LINE = "BOND";
const String BOND_LINE2 = "DOUBLE";
const String ANGLE_LINE = "ANGL";
const String ANGLE_LINE2 = "THET";
const String DIHEDRAL_LINE = "DIHE";
const String DIHEDRAL_LINE2 = "PHI";
const String IMPROPER_LINE = "IMPR";
const String IMPROPER_LINE2 = "IMPH";
const String IC_LINE = "IC";
std::string first_patch = "", last_patch = "";
Pointer<CHARMMIdealResidueTopology> residue;
Pointer<CHARMMPatch> patch;
ResidueType curr_res_type;
while (!input_file.get_stream().eof()) {
String line;
getline(input_file.get_stream(), line);
boost::trim(line); // remove all spaces
// skip comments or empty lines
if (line[0] == '!' || line[0] == '*' || line.length() == 0) continue;
// read residue line
if(line.substr(0, RESI_LINE.length()) == RESI_LINE) {
if (residue) {
add_residue_topology(residue.release());
} else if (patch) {
add_patch(patch.release());
}
curr_res_type = parse_residue_line(line, translate_names_to_pdb);
ResidueType rt(curr_res_type.get_string());
residue = new CHARMMIdealResidueTopology(rt);
residue->set_default_first_patch(first_patch);
residue->set_default_last_patch(last_patch);
// handle patch residues
} else if (line.substr(0, PRES_LINE.length()) == PRES_LINE) {
if (residue) {
add_residue_topology(residue.release());
} else if (patch) {
add_patch(patch.release());
}
Strings split_results;
boost::split(split_results, line, boost::is_any_of(" \t"),
boost::token_compress_on);
if (split_results.size() < 3) {
IMP_THROW("Invalid PRES line: " << line, ValueException);
}
patch = new CHARMMPatch(get_residue_name(split_results[1],
translate_names_to_pdb));
// handle MASS line
} else if (line.substr(0, MASS_LINE.length()) == MASS_LINE) {
parse_mass_line(line, atom_type_to_element_);
// handle DEFA line
} else if (line.substr(0, DEFA_LINE.length()) == DEFA_LINE) {
parse_patch_line(line, first_patch, last_patch, translate_names_to_pdb);
// handle PATC line
} else if (line.substr(0, PATC_LINE.length()) == PATC_LINE
&& residue) {
std::string first = residue->get_default_first_patch();
std::string last = residue->get_default_last_patch();
parse_patch_line(line, first, last, translate_names_to_pdb);
residue->set_default_first_patch(first);
residue->set_default_last_patch(last);
// read DELE line
} else if (line.substr(0, DELE_LINE.length()) == DELE_LINE
&& patch) {
parse_dele_line(line, patch, translate_names_to_pdb);
// read atom line
} else if (line.substr(0, ATOM_LINE.length()) == ATOM_LINE
&& (residue || patch)) {
parse_atom_line(line, curr_res_type, get_residue(residue, patch),
translate_names_to_pdb);
// read bond line
} else if ((line.substr(0, BOND_LINE.length()) == BOND_LINE ||
line.substr(0, BOND_LINE2.length()) == BOND_LINE2)
&& (residue || patch)) {
parse_bond_line(line, curr_res_type, get_residue(residue, patch),
translate_names_to_pdb);
// read angle line
} else if ((line.substr(0, ANGLE_LINE.length()) == ANGLE_LINE ||
line.substr(0, ANGLE_LINE2.length()) == ANGLE_LINE2)
&& (residue || patch)) {
parse_angle_line(line, get_residue(residue, patch),
translate_names_to_pdb);
// read dihedral line
} else if ((line.substr(0, DIHEDRAL_LINE.length()) == DIHEDRAL_LINE ||
line.substr(0, DIHEDRAL_LINE2.length()) == DIHEDRAL_LINE2)
&& (residue || patch)) {
parse_dihedral_line(line, get_residue(residue, patch),
translate_names_to_pdb);
// read improper line
} else if ((line.substr(0, IMPROPER_LINE.length()) == IMPROPER_LINE ||
line.substr(0, IMPROPER_LINE2.length()) == IMPROPER_LINE2)
&& (residue || patch)) {
parse_improper_line(line, get_residue(residue, patch),
translate_names_to_pdb);
// read internal coordinate line
} else if (line.substr(0, IC_LINE.length()) == IC_LINE
&& (residue || patch)) {
parse_internal_coordinate_line(line, get_residue(residue, patch),
translate_names_to_pdb);
}
}
if (residue) {
add_residue_topology(residue);
} else if (patch) {
add_patch(patch);
}
}
int main(int argc, char *argv[]){
MPI_Init(&argc, &argv);
MPI_Comm_split_type(MPI_COMM_WORLD, MPI_COMM_TYPE_SHARED, 0, MPI_INFO_NULL, &shmcomm);
MPI_Comm_size(MPI_COMM_WORLD, &numprocs);
MPI_Comm_rank(MPI_COMM_WORLD, &myid);
double t_begin;
int i, j, k, ii, id, id1;
t_begin = MPI_Wtime(); // record the begining CPU time
read_param();
lattice_vec();
allocate();
p_allocate();
if (flow_on!=0) {
build_stream();
}
if (Q_on!=0) {
build_neighbor();
}
init_surf();
add_patch();
p_init();
p_iden();
init();
if (flow_on!=0) cal_fequ(f);
if (Q_on!=0) cal_dQ();
if (Q_on!=0 && flow_on!=0 && newrun_on!=0) {
while(qconverge==0) {
t_current++;
for (ii=0; ii<n_evol_Q; ii++) {
cal_dQ();
evol_Q();
}
if (t_current%t_print==0) monitor();
}
e_tot =-1;
k_eng =-1;
qconverge = 0;
uconverge = 0;
t_current =-1;
}
if (Q_on!=0 && flow_on!=0) {
cal_W();
cal_stress();
cal_sigma_p();
}
MPI_Barrier(MPI_COMM_WORLD);
output1(1,'z',Nx/2,Ny/2);
output3(1);
if(myid==0) printf("Q initialized\n");
MPI_Barrier(MPI_COMM_WORLD);
while (t_current<t_max && uconverge*qconverge==0) {
e_toto=e_tot;
if (Q_on!=0 && qconverge==0) {
if (flow_on!=0 && uconverge==0) cal_W();
for (ii=0; ii<n_evol_Q; ii++) {
cal_dQ();
evol_Q();
}
}
if (flow_on!=0 && uconverge==0) {
if (Q_on!=0 && qconverge==0) {
cal_stress();
cal_sigma_p();
}
evol_f(f,f2);
}
if (Q_on!=0 && qconverge==0) {
if (flow_on!=0 && uconverge==0) cal_W();
for (ii=0; ii<n_evol_Q; ii++) {
cal_dQ();
evol_Q();
}
}
if (flow_on!=0 && uconverge==0) {
if (Q_on!=0 && qconverge==0) {
cal_stress();
cal_sigma_p();
}
evol_f(f2,f);
}
if (t_current%t_print==0) monitor();
if (t_current%t_write==0) {
output1(0,'z',Nx/2,Ny/2);
output3(0);
fflush(stdout);
}
t_current++;
}
output_time(t_begin);
output1(0,'z',Nx/2,Ny/2);
output3(0);
write_restart();
p_deallocate();
deallocate();
return 0;
}
int WitnessSet::Parse(const boost::filesystem::path witness_set_file, const int num_vars)
{
FILE *IN = safe_fopen_read(witness_set_file);
int temp_num_patches, patch_size, temp_num_linears, temp_num_points, num_vars_in_linears;
fscanf(IN, "%d %d %d", &temp_num_points, &dim_, &comp_num_); scanRestOfLine(IN);
this->num_vars_ = num_vars;
this->num_natty_vars_ = num_vars;
vec_mp temp_vec; init_vec_mp2(temp_vec, num_vars,1024); temp_vec->size = num_vars;
for (int ii=0; ii < temp_num_points; ii++) {
//read the witness points into memory
for (int jj=0; jj < num_vars; ++jj) {
mpf_inp_str(temp_vec->coord[jj].r, IN, 10); // 10 is the base
mpf_inp_str(temp_vec->coord[jj].i, IN, 10);
scanRestOfLine(IN);
}
add_point(temp_vec);
}
fscanf(IN, "%d %d", &temp_num_linears, &num_vars_in_linears); scanRestOfLine(IN);
for (int ii=0; ii < temp_num_linears; ii++) {
change_size_vec_mp(temp_vec,num_vars_in_linears);
temp_vec->size = num_vars_in_linears;
//read the witness linears into memory
for (int jj=0; jj < num_vars_in_linears; jj++) {
mpf_inp_str(temp_vec->coord[jj].r, IN, 10);
mpf_inp_str(temp_vec->coord[jj].i, IN, 10);
scanRestOfLine(IN);
}
add_linear(temp_vec);
}
fscanf(IN, "%d %d", &temp_num_patches, &patch_size); scanRestOfLine(IN);
if (temp_num_patches>1) {
std::cerr << temp_num_patches << " patches detected. this probably indicates a problem." << std::endl;
std::cerr << "the file being read: " << witness_set_file << std::endl;
std::cerr << "trying to read " << num_vars << " variables." << std::endl;
mypause();
}
for (int ii=0; ii < temp_num_patches; ii++) {
change_size_vec_mp(temp_vec,patch_size);
temp_vec->size = patch_size;
//read the patch into memory
for (int jj=0; jj < patch_size; jj++) {
mpf_inp_str(temp_vec->coord[jj].r, IN, 10);
mpf_inp_str(temp_vec->coord[jj].i, IN, 10);
scanRestOfLine(IN);
}
add_patch(temp_vec);
}
fclose(IN);
clear_vec_mp(temp_vec);
return 0;
}
