void SaveOptPdb(char szName[])
{
int i;
for(i=0; i<n_Phi; i++) {
Mol.QueryDihedral(IdxDihSelect[i]);
Mol.Edit_Dihedral(IdxDihSelect[i], Phi_To_Set_Scan[i]);
}
Mol.SavePdb(szName);
}
void MM_Fixed_1D_Scan(void)
{
int i, Phi, Count;
RestoreCoordinates();
for(i=0; i<n_Phi; i++) {
Mol.QueryDihedral(IdxDihSelect[i]);
Mol.Edit_Dihedral(IdxDihSelect[i], Phi_To_Set[i]);
}
Count = 0;
for(Phi=-180; Phi<=180; Phi+=BIN_SIZE) { // 1D scan for this rotamer
Phi_To_Set[Active_Phi] = Phi*1.0;
Mol.QueryDihedral(IdxDihSelect[Active_Phi]);
Mol.Edit_Dihedral(IdxDihSelect[Active_Phi], Phi_To_Set[Active_Phi]);
E_Phi[Count] = Mol.Cal_E(0);
Count++;
}
return;
}
void Output_Gaussian_File(void)
{
FILE *fOut, *fIn;
int i, nAtom, IdxScan;
char szNameGjf[256], szCmd[256], szName_Output[256];
Determine_QM_Scan_Part();
nAtom = Mol.nAtom;
for(IdxScan=0; IdxScan<n_QM_Part; IdxScan++) {
Mol.QueryDihedral(IdxDihSelect[Active_Phi]);
Mol.Edit_Dihedral(IdxDihSelect[Active_Phi], Phi_QM_Start[IdxScan]);
sprintf(szNameGjf, "qm-scan-%d-%d.gjf", Active_Phi+1, IdxScan+1);
fOut = fopen(szNameGjf, "w");
fprintf(fOut, "%s", szQM_Level_1D_Scan_Cmd);
for(i=0; i<nAtom; i++) {
// fprintf(fOut, "%c %9.5lf %9.5lf %9.5lf\n", Mol.AtomName[i][0], Mol.x[i], Mol.y[i], Mol.z[i]);
fprintf(fOut, "%s %9.5lf %9.5lf %9.5lf\n", szElemName[i], Mol.x[i], Mol.y[i], Mol.z[i]);
}
fprintf(fOut, "\n");
for(i=0; i<n_Phi; i++) {
if(i == Active_Phi) {
fprintf(fOut, "%s", szQM_Scan[IdxScan]);
}
else {
fprintf(fOut, "%d %d %d %d F\n", DihList[i][0]+1, DihList[i][1]+1, DihList[i][2]+1, DihList[i][3]+1);
}
}
fprintf(fOut, "\n");
fclose(fOut);
sprintf(szName_Output, "qm-1d-phi-%d-p%d.out", Active_Phi+1, IdxScan+1);
sprintf(szCmd, "%s < %s > %s", szExe_G09, szNameGjf, szName_Output);
fIn = fopen(szName_Output, "r");
if(fIn == NULL) {
system(szCmd);
}
else {
fclose(fIn);
}
Extract_Coord_E(szName_Output, Active_Phi, IdxScan);
}
}
int main(int argc, char **argv)
{
int i;
FILE *fOut;
char szName[256];
fFile_Run_Log = fopen("qm-1d-scan.log", "w");
// MPI_Init(&argc, &argv);
// MPI_Comm_rank(MPI_COMM_WORLD, &ProgID);
// MPI_Comm_size(MPI_COMM_WORLD, &nProc);
Get_EXE_Path("G09_EXE_PATH", szExe_G09);
n_Bins = 360/BIN_SIZE+1;
ForceField.ReadForceField(szForceFiled);
Mol.ReadPSF(szXpsfFile, 0);
Get_Netcharge_From_Xpsf();
Setup_QM_Level();
ReadElementList();
Mol.AssignForceFieldParameters(&ForceField);
Mol.ReadCRD(szCrdFile);
BackupCoordinates();
Read_Soft_DihedralList();
for(Active_Phi=0; Active_Phi<n_Phi; Active_Phi++) {
RestoreCoordinates();
for(i=0; i<n_Phi; i++) {
Phi_To_Set[i] = Mol.QueryDihedral(IdxDihSelect[i]);
Mol.Edit_Dihedral(IdxDihSelect[i], Phi_To_Set[i]);
}
MM_Fixed_1D_Scan();
E_Barrier_Lowest = Get_Barrier(E_Phi, n_Bins, E_Min, Phi_Save);
E_Min_Save = E_Min;
E_Min_Org = E_Min + E_RANGE;
memcpy(E_Scan, E_Phi, sizeof(double)*n_Bins);
memcpy(Phi_To_Set_Scan, Phi_To_Set, sizeof(double)*n_Phi);
Phi_To_Set_Scan[Active_Phi] = Phi_Save;
sprintf(szName, "ini-%d.dat", Active_Phi+1);
fOut = fopen(szName, "w");
for(i=0; i<n_Bins; i++) {
fprintf(fOut, "%5d %8.5E\n", -180+i*BIN_SIZE, E_Scan[i]-E_Min);
}
fclose(fOut);
sprintf(szName, "ini-%d.pdb", Active_Phi+1);
SaveOptPdb(szName);
n_State_List[Active_Phi] = 1;
Enumerate_Dihedrals(0);
n_State_List[Active_Phi] = n_State_List_Save[Active_Phi];
sprintf(szName, "end-%d.dat", Active_Phi+1);
fOut = fopen(szName, "w");
for(i=0; i<n_Bins; i++) {
fprintf(fOut, "%5d %8.5E\n", -180+i*BIN_SIZE, E_Scan[i]-E_Min_Save);
}
fclose(fOut);
sprintf(szName, "end-%d.pdb", Active_Phi+1);
SaveOptPdb(szName);
sprintf(szName, "phi-%d.dat", Active_Phi+1);
fOut = fopen(szName, "w");
for(i=0; i<n_Phi; i++) {
fprintf(fOut, "%lf\n", Phi_To_Set_Scan[i]);
}
fclose(fOut);
Output_Gaussian_File();
}
Reorganize_QM_1D_Scan_Data();
fclose(fFile_Run_Log);
// MPI_Barrier(MPI_COMM_WORLD);
// MPI_Finalize();
return 0;
}
int main(int argc, char **argv)
{
int i;
FILE *fOut;
char szName[256], *szEnv;
// SetEnvironmentVariable(szGAUSS_SCRDIR, "c:\\1");
fFile_Run_Log = fopen("qm-1d-scan.log", "w");
szEnv = getenv(szGAUSS_SCRDIR);
if (szEnv == NULL) {
Quit_With_Error_Msg("Environment variable $GAUSS_SCRDIR is NOT set.\nQuit\n");
}
strcpy(szGAUSS_SCRDIR_Base, szEnv);
Get_EXE_Path("G09_EXE_PATH", szExe_G09);
n_Bins = 360/BIN_SIZE+1;
ForceField.ReadForceField(szForceFiled);
Mol.ReadPSF(szXpsfFile, 0);
Get_Netcharge_From_Xpsf();
Setup_QM_Level();
ReadElementList();
Mol.AssignForceFieldParameters(&ForceField);
Mol.ReadCRD(szCrdFile);
BackupCoordinates();
Read_Soft_DihedralList();
nJob = nJobDone = 0;
for(Active_Phi=0; Active_Phi<n_Phi; Active_Phi++) {
RestoreCoordinates();
for(i=0; i<n_Phi; i++) {
Phi_To_Set[i] = Mol.QueryDihedral(IdxDihSelect[i]);
Mol.Edit_Dihedral(IdxDihSelect[i], Phi_To_Set[i]);
}
MM_Fixed_1D_Scan();
E_Barrier_Lowest = Get_Barrier(E_Phi, n_Bins, E_Min, Phi_Save);
E_Min_Save = E_Min;
E_Min_Org = E_Min + E_RANGE;
memcpy(E_Scan, E_Phi, sizeof(double)*n_Bins);
memcpy(Phi_To_Set_Scan, Phi_To_Set, sizeof(double)*n_Phi);
Phi_To_Set_Scan[Active_Phi] = Phi_Save;
sprintf(szName, "ini-%d.dat", Active_Phi+1);
fOut = fopen(szName, "w");
for(i=0; i<n_Bins; i++) {
fprintf(fOut, "%5d %8.5E\n", -180+i*BIN_SIZE, E_Scan[i]-E_Min);
}
fclose(fOut);
sprintf(szName, "ini-%d.pdb", Active_Phi+1);
SaveOptPdb(szName);
n_State_List[Active_Phi] = 1;
Enumerate_Dihedrals(0);
n_State_List[Active_Phi] = n_State_List_Save[Active_Phi];
sprintf(szName, "end-%d.dat", Active_Phi+1);
fOut = fopen(szName, "w");
for(i=0; i<n_Bins; i++) {
fprintf(fOut, "%5d %8.5E\n", -180+i*BIN_SIZE, E_Scan[i]-E_Min_Save);
}
fclose(fOut);
sprintf(szName, "end-%d.pdb", Active_Phi+1);
SaveOptPdb(szName);
sprintf(szName, "phi-%d.dat", Active_Phi+1);
fOut = fopen(szName, "w");
for(i=0; i<n_Phi; i++) {
fprintf(fOut, "%lf\n", Phi_To_Set_Scan[i]);
}
fclose(fOut);
Output_Gaussian_File();
}
if(nJob > 0) {
RunAllJobs();
Exatract_All_Info_QM_1D_Scan();
Reorganize_QM_1D_Scan_Data();
}
fclose(fFile_Run_Log);
return 0;
}