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);
}
}
void Reorganize_QM_1D_Scan_Data(void)
{
FILE *fIn, *fOut, *fQMStates;
int i, j, i_Left, i_Right, Idx_Phi, nScan, nScan_Mapped, ReadItem, nAtom, To_Output[MAX_SCAN];
char szName_Input[256], szName_Output[256], ErrorMsg[256], szLine[256], *ReadLine, szTmp[256];
double x_List[MAX_SCAN][MAX_ATOM], y_List[MAX_SCAN][MAX_ATOM], z_List[MAX_SCAN][MAX_ATOM];
double E_QM[MAX_SCAN], E_MM[MAX_SCAN], Phi[MAX_SCAN], Phi_Mapped[MAX_SCAN], E_QM_Mapped[MAX_SCAN], E_Min, E_Max, Phi_Ini, fTmp=0.0;
int N_Rotamer_Total=1, nState, DoubleBond;
RestoreCoordinates();
nAtom = Mol.nAtom;
fQMStates = fopen("qm-1d-states.dat", "w");
for(Idx_Phi=0; Idx_Phi<n_Phi; Idx_Phi++) {
sprintf(szName_Input, "tor-1D-idx-%d.dat", Idx_Phi+1);
sprintf(szName_Output, "new-tor-1D-idx-%d.dat", Idx_Phi+1);
E_Min = 1.0E100;
E_Max = -1.0E100;
Phi_Ini = Mol.QueryDihedral(IdxDihSelect[Idx_Phi]);
DoubleBond = Is_This_A_Double_Bond(DihList[Idx_Phi][1], DihList[Idx_Phi][2]);
nScan = 0;
fIn = fopen(szName_Input, "r");
if(fIn == NULL) {
sprintf(ErrorMsg, "Fail to open file for read: %s\nQuit\n", szName_Input);
Quit_With_Error_Msg(ErrorMsg);
}
while(1) {
if(feof(fIn)) {
break;
}
ReadLine = fgets(szLine, 256, fIn);
if(ReadLine == NULL) {
break;
}
if(strncmp(szLine, "E_Scan", 6) == 0) {
ReadItem = sscanf(szLine, "%s %lf %lf %s %lf", szTmp, &(E_QM[nScan]), &(E_MM[nScan]), szTmp, &(Phi[nScan]));
if(ReadItem == 5) {
fgets(szLine, 256, fIn);
for(i=0; i<nAtom; i++) {
fgets(szLine, 256, fIn);
ReadItem = sscanf(szLine, "%lf %lf %lf", &(x_List[nScan][i]), &(y_List[nScan][i]), &(z_List[nScan][i]));
if(ReadItem != 3) {
fclose(fIn);
sprintf(ErrorMsg, "Error in readubg file: %s\nQuit\n", szName_Input);
Quit_With_Error_Msg(ErrorMsg);
}
}
if(E_QM[nScan] < E_Min) {
E_Min = E_QM[nScan];
}
if(E_QM[nScan] > E_Max) {
E_Max = E_QM[nScan];
}
nScan++;
}
else {
break;
}
}
}
fclose(fIn);
for(i=0; i<nScan; i++) {
To_Output[i] = 1;
}
if( (Phi[0] > 0.0) && (Cal_Phi_Dist(Phi[0], -180.0) < 1.0) ) { // +180.0 at the first point
Phi[0] -= 360.0;
}
//start to delete those redundant entries
for(i=0; i<nScan; i++) {
for(j=i+1; j<nScan; j++) {
if(Cal_Phi_Dist(Phi[i], Phi[j]) < 1.0) { // the same dihedral
if(Cal_Phi_Dist(Phi[j], -180.0) > 1.0) { // only -180, 180 can exist, others will be removed
To_Output[j] = 0;
}
}
}
}
//end to delete those redundant entries
//start to set the correct sign of +180 if it exists as -180
if(Cal_Phi_Dist(Phi[0], -180.0) < 1.0) { // starting with -180
for(i=nScan-1; i>0; i--) {
if(To_Output[i] == 0) {
continue;
}
if( (Phi[i] < 0.0) && (Cal_Phi_Dist(Phi[i], -180.0) < 1.0) ) {
Phi[i] += 360.0;
// break;
}
}
}
//end to set the correct sign of +180 if it exists as -180
// fOut = fopen(szName_Output, "w");
fOut = fopen(szName_Input, "w"); // to overwrite
for(j=0; j<nScan; j++) {
if(To_Output[j]==0) {
continue;
}
fprintf(fOut, "E_Scan %.13E %.13E Phi %.1lf\n", E_QM[j], E_MM[j], Phi[j]);
fprintf(fOut, "Coordinate\n");
for(i=0; i<nAtom; i++) {
fprintf(fOut, "%12.6lf %12.6lf %12.6lf\n", x_List[j][i], y_List[j][i], z_List[j][i]);
}
}
fclose(fOut);
//start to identify QM local minima of each dihedral
nScan_Mapped = 0;
for(i=0; i<nScan; i++) {
if(To_Output[i]) {
if(fabs(Phi[i]-180.0) > 3.0) { // +180 is excluded
Phi_Mapped[nScan_Mapped] = Phi[i];
E_QM_Mapped[nScan_Mapped] = E_QM[i];
nScan_Mapped++;
}
}
}
if(nScan_Mapped < 3) {
sprintf(ErrorMsg, "nScan_Mapped < 3 for dihedral %d \nQuit\n", Idx_Phi+1);
Quit_With_Error_Msg(ErrorMsg);
}
fprintf(fQMStates, "%3d %3d %3d %3d ", DihList[Idx_Phi][0]+1, DihList[Idx_Phi][1]+1, DihList[Idx_Phi][2]+1, DihList[Idx_Phi][3]+1);
nState = 0;
for(i=0; i<nScan_Mapped; i++) {
i_Left = (i+nScan_Mapped-1)%nScan_Mapped;
i_Right = (i+nScan_Mapped+1)%nScan_Mapped;
if( (DoubleBond) && ( ((E_Max-E_Min)*HARTREE_KCAL) > E_BARRIER_DOUBLE_BOND ) ) {
fprintf(fQMStates, " %.0lf", Phi_Ini);
nState = 1;
break;
}
if( (E_QM_Mapped[i] <= E_QM_Mapped[i_Left]) && (E_QM_Mapped[i] <= E_QM_Mapped[i_Right]) ) { // a local minimum along QM 1D profile
fprintf(fQMStates, " %.0lf", Phi_Mapped[i]);
nState++;
}
}
fprintf(fQMStates, "\n");
N_Rotamer_Total *= nState;
//end to identify QM local minima of each dihedral
}
fclose(fQMStates);
fOut = fopen("n_rotamer.txt", "w");
fprintf(fOut, "%d", N_Rotamer_Total);
fclose(fOut);
}
void Extract_Coord_E(char szName[], int Idx_Phi, int Idx_Part)
{
FILE *fIn, *fOut;
int i, nAtom, ToRead=1, ReadItem, n_Rec=0;
char szOutput[256], szErrorMsg[256], szLine[256], *ReadLine, szTag[256], ErrorMsg[256];
double E_QM, E_MM, Phi, Phi_Set, x_Save[MAX_ATOM], y_Save[MAX_ATOM], z_Save[MAX_ATOM];
nAtom = Mol.nAtom;
memcpy(x_Save, Mol.x, sizeof(double)*nAtom);
memcpy(y_Save, Mol.y, sizeof(double)*nAtom);
memcpy(z_Save, Mol.z, sizeof(double)*nAtom);
sprintf(szOutput, "tor-1D-idx-%d.dat", Idx_Phi+1);
fOut = fopen(szOutput, "a+");
fseek(fOut, 0, SEEK_END);
fIn = fopen(szName, "r");
if(fIn == NULL) {
sprintf(szErrorMsg, "Fail to open %s\nQuit\n", szName);
Quit_With_Error_Msg(szErrorMsg);
}
while(ToRead) {
if(feof(fIn)) {
break;
}
ReadLine = fgets(szLine, 256, fIn);
if(ReadLine == NULL) {
break;
}
else {
// if(FindString(szLine, " Center Atomic Atomic")>=0) { // to extract the coordinate
// Skip_N_Line(fIn, szName, 2);
// if(FindString(szLine, " Input orientation:")>=0) { // to extract the coordinate
if(FindString(szLine, " orientation:")>=0) { // to extract the coordinate
Skip_N_Line(fIn, szName, 4);
for(i=0; i<nAtom; i++) {
ReadLine = fgets(szLine, 256, fIn);
if(ReadLine == NULL) {
break;
}
ReadItem = sscanf(szLine+31, "%lf %lf %lf", &(Mol.x[i]), &(Mol.y[i]), &(Mol.z[i]));
if(ReadItem != 3) {
ToRead = 0;
break;
}
}
}
else if( (FindString(szLine, " SCF Done: ")>=0) && (QM_Level == QM_LEVEL_HF) ) { // HF
E_QM = Get_Energy(szLine);
}
else if( (FindString(szLine, "EUMP2 =")>=0) && (QM_Level == QM_LEVEL_MP2) ) {
E_QM = Get_Energy(szLine+27);
}
else if(FindString(szLine, " Optimization completed")>=0) {
sprintf(szTag, " D(%d,%d,%d,%d)", DihList[Idx_Phi][0]+1, DihList[Idx_Phi][1]+1, DihList[Idx_Phi][2]+1, DihList[Idx_Phi][3]+1);
To_Find_Tag(fIn, szName, szTag, szLine);
ReadItem = sscanf(szLine+28, "%lf", &Phi_Set); // previous, modredundant
if(ReadItem != 1) {
sprintf(ErrorMsg, "Error in extracting the dihedral.\n%s\nQuit\n", szLine);
Quit_With_Error_Msg(ErrorMsg);
}
Phi = Mol.QueryDihedral(IdxDihSelect[Idx_Phi]);
E_MM = Mol.Cal_E(0);
fprintf(fOut, "E_Scan %.13E %.13E Phi %.1lf\n", E_QM, E_MM, Phi);
fprintf(fOut, "Coordinate\n");
for(i=0; i<nAtom; i++) {
fprintf(fOut, "%12.6lf %12.6lf %12.6lf\n", Mol.x[i], Mol.y[i], Mol.z[i]);
}
n_Rec++;
}
}
}
fclose(fOut);
fclose(fIn);
memcpy(Mol.x, x_Save, sizeof(double)*nAtom);
memcpy(Mol.y, y_Save, sizeof(double)*nAtom);
memcpy(Mol.z, z_Save, sizeof(double)*nAtom);
}
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;
}