void Add_Tip3_Prm_File(void)
{
FILE *fOut;
char *ReadLine, ErrorMsg[256];
int i;
Found_Improper = 0;
fOut = fopen(szPrmFile, "r");
if(fOut == NULL) {
sprintf(ErrorMsg, "Error in open file: %s\nQuit\n", szPrmFile);
Quit_With_Error_Msg(ErrorMsg);
}
else {
n_Line = 0;
while(1) {
if(feof(fOut)) {
break;
}
ReadLine = fgets(szTxtPrm[n_Line], MAX_LEN, fOut);
To_Upper_Case(szTxtPrm[n_Line]);
if(ReadLine == NULL) {
break;
}
else {
if(strncmp(szTxtPrm[n_Line], "BOND", 4)==0) {
sprintf(szTxtPrm[n_Line], "BONDS\n"); // rename "BOND" to "BONDS"
}
else if(strncmp(szTxtPrm[n_Line], "ANGLE", 5)==0) {
sprintf(szTxtPrm[n_Line], "ANGLES\n"); // rename "ANGLE" to "ANGLES"
Line_Insert_Bond = n_Line;
}
else if(strncmp(szTxtPrm[n_Line], "DIHEDRAL", 8)==0) {
sprintf(szTxtPrm[n_Line], "DIHEDRALS\n"); // rename "DIHEDRAL" to "DIHEDRALS"
Line_Insert_Angle = n_Line;
}
else if(strncmp(szTxtPrm[n_Line], "IMPHI", 5)==0) {
Found_Improper = 1;
sprintf(szTxtPrm[n_Line], "IMPROPERS\n"); // rename "IMPHI" to "IMPROPERS"
}
else if(strncmp(szTxtPrm[n_Line], "IMPROPER", 8)==0) {
Found_Improper = 1;
sprintf(szTxtPrm[n_Line], "IMPROPERS\n"); // rename "IMPHI" to "IMPROPERS"
}
else if(strncmp(szTxtPrm[n_Line], "NONBONDED", 9)==0) {
Line_Insert_Impropers = n_Line;
}
if(strncmp(szTxtPrm[n_Line], "END", 3)==0) {
continue;
}
n_Line++;
if(n_Line >= MAX_LINE) {
sprintf(ErrorMsg, "n_Line >= MAX_LINE\nQuit\n");
fclose(fOut);
Quit_With_Error_Msg(ErrorMsg);
}
}
}
fclose(fOut);
}
fOut = fopen(szPrmFile, "w");
for(i=0; i<n_Line; i++) {
if(i == Line_Insert_Bond) {
fprintf(fOut, "HT_W HT_W 0.000 1.5139 ! FROM TIPS3P GEOMETRY (FOR SHAKE/W PARAM)\n");
fprintf(fOut, "OT_W HT_W 450.000 0.9572 ! FROM TIPS3P GEOM\n\n");
}
else if(i == Line_Insert_Angle) {
fprintf(fOut, "HT_W OT_W HT_W 55.000 104.5200 ! TIP3P GEOMETRY\n\n");
}
else if( (Found_Improper==0) && (i==Line_Insert_Impropers) ) { // add the entry for IMPROPERS
fprintf(fOut, "IMPROPERS\n\n");
}
if(FindString(szTxtPrm[i], "NONBONDED") >= 0) {
fprintf(fOut, "NONBONDED E14FAC %9.6lf\n", E14FAC);
continue;
}
else if(FindString(szTxtPrm[i], "NBXMOD") >= 0) {
continue;
}
else if(FindString(szTxtPrm[i], "CUTNB") >= 0) {
continue;
}
else if(FindString(szTxtPrm[i], "E14FAC") >= 0) {
continue;
}
else if(FindString(szTxtPrm[i], "WMIN") >= 0) {
continue;
}
fprintf(fOut, "%s", szTxtPrm[i]);
}
fprintf(fOut, "\nHT_W 0.000000 -0.046000 0.224500 ! TIP3P HYDROGEN PARAMETERS, adm jr., NBFIX obsolete\n");
fprintf(fOut, "OT_W 0.000000 -0.152100 1.768200 ! TIP3P OXYGEN PARAMETERS, adm jr., NBFIX obsolete\n\n");
// fprintf(fOut, "\n\nEND\n");
fclose(fOut);
}
int main(int argc, char **argv)
{
char ErrorMsg[256];
fFile_Run_Log = fopen(szName_Run_Log, "w");
if(fFile_Run_Log==NULL) {
sprintf(ErrorMsg, "Fail to create the log file.\n\n");
Quit_With_Error_Msg(ErrorMsg);
}
strcpy(szName_Conf_File, argv[1]);
ReadConfFile(szName_Conf_File);
// MPI_Init(&argc, &argv);
// MPI_Comm_rank(MPI_COMM_WORLD, &ProgID);
// MPI_Comm_size(MPI_COMM_WORLD, &nProc);
ForceField.ReadForceField(szName_Force_Field);
Mol_ESP.ReadPSF(szName_XPSF, 0);
Read_Rtf_File();
strcpy(Mol_ESP.MolName, Mol_ESP.ResName[0]);
Mol_ESP.AssignForceFieldParameters(&ForceField);
Read_Soft_DihedralList();
Mol_ESP.Is_Phi_Psi_Constrained = 0;
Mol_ESP.E_CMap_On = 0;
Read_QM_Rotamer_Data();
// Read_Tor_Para_1D_Fitting();
// Assign_Torsion_Parameters();
// Read_1D_Scan_QM_Data();
// Cal_E_MM_Scaned();
Cal_E_MM_Rotamer();
Output_Rotamer_QM_MM();
// fFitting = fopen("fitting.dat", "w");
// Fitting_Torsion_Parameters();
// fclose(fFitting);
// FILE *fOut;
// fOut = fopen("rotamer-E.dat", "w");
// for(i=0; i<nRotamer; i++) {
// fprintf(fOut, "%d %lf %lf %lf\n", i+1, E_Rotamer_QM[i], E_Rotamer_MM[i], rmsd_Rotamer[i]);
// }
// fclose(fOut);
// Cal_E_MM_QM_Diff(7);
// for(i=0; i<n_Phi; i++) {
// Cal_E_MM_QM_Diff(i);
// }
// Fit_Torsion_Parameters(7);
// fPara = fopen("torsion-para.dat", "w");
// for(i=0; i<n_Phi; i++) {
// Fit_Torsion_Parameters(i);
// }
// fclose(fPara);
// Geoometry_Optimization_With_Constraint(&Mol_ESP);
fflush(fFile_Run_Log);
fclose(fFile_Run_Log);
// MPI_Finalize();
return 0;
}
void Cal_E_MM_QM_Diff(int Idx)
{
FILE *fIn, *fOut;
char szName[256], szLine[256], *ReadLine, szTmp[256], ErrorMsg[256];
double E_QM_Min, E_MM_Min, E_MM_Read, E_MM_Cal;
double Para_k_Dih_Save[6], Para_phi_Dih_Save[6];
double x_Save[MAX_NUM_ATOM], y_Save[MAX_NUM_ATOM], z_Save[MAX_NUM_ATOM];
int i, j, ReadItem, nAtom;
memcpy(Para_k_Dih_Save, Mol_ESP.Para_k_Dih[IdxDihSelect[Idx]]+1, sizeof(double)*6);
memcpy(Para_phi_Dih_Save, Mol_ESP.Para_phi[IdxDihSelect[Idx]]+1, sizeof(double)*6);
memset(Mol_ESP.Para_k_Dih[IdxDihSelect[Idx]]+1, 0, sizeof(double)*6); // turn of this dihedral
memset(Mol_ESP.Para_phi[IdxDihSelect[Idx]]+1, 0, sizeof(double)*6);
sprintf(szName, "tor-1D-idx-%d.dat", Idx+1);
fIn = fopen(szName, "r");
if(fIn == NULL) {
sprintf(ErrorMsg, "Fail to open file: %s\nQuit\n", szName);
printf("%s", ErrorMsg);
Quit_With_Error_Msg(ErrorMsg);
}
sprintf(szName, "mm-tor-1D-idx-%d.dat", Idx+1); // the one with optimized geometry in MM force field
fOut = fopen(szName, "w");
nAtom = Mol_ESP.nAtom;
nScan = 0;
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_Scaned[nScan]), &E_MM_Read, szTmp, &(Phi_Scaned[nScan]));
if(ReadItem != 5) {
sprintf(ErrorMsg, "Error in reading file: %s\nQuit\n", szName);
Quit_With_Error_Msg(ErrorMsg);
}
ReadLine = fgets(szLine, 256, fIn); // skip one line, "Coordinate"
for(i=0; i<nAtom; i++) { // read one snapshot
ReadLine = fgets(szLine, 256, fIn);
ReadItem = sscanf(szLine, "%lf %lf %lf", &(Mol_ESP.x[i]), &(Mol_ESP.y[i]), &(Mol_ESP.z[i]));
}
E_MM_Cal = Mol_ESP.Cal_E(0); // the nergy without optimization and dihedral term is turned off
To_Setup_All_Dihedral_Constraint();
E_MM_Scaned[nScan] = Geoometry_Optimization_With_Constraint(&Mol_ESP); // do restrained geometry optimizatio. soft restraint on all dihedrals. Rigid restraints on soft dihedrals
if(E_MM_Scaned[nScan] > (1.0E3+E_MM_Cal)) { // not a valid configuration. Something wrong in the constrained optimization
printf(" Bad configuration: %d %f %f\n", nScan, E_MM_Scaned[nScan], E_MM_Cal );
continue;
}
memcpy(x_Save, Mol_ESP.x, sizeof(double)*nAtom);
memcpy(y_Save, Mol_ESP.y, sizeof(double)*nAtom);
memcpy(z_Save, Mol_ESP.z, sizeof(double)*nAtom);
fprintf(fOut, "E_Scan %.13E %.13E Phi %.1lf\n", E_QM_Scaned[nScan], E_MM_Scaned[nScan], Phi_Scaned[nScan]);
fprintf(fOut, "Coordinate\n");
for(j=0; j<nAtom; j++) {
fprintf(fOut, "%14.6lf%14.6lf%14.6lf\n", x_Save[j], y_Save[j], z_Save[j]);
}
// fprintf(fOut, "%.1lf %.6lf %.6lf %.6lf\n", Phi_Scaned[i], E_QM_Scaned[i], E_MM_Scaned[i], E_QM_Scaned[i] - E_MM_Scaned[i]);
nScan++;
}
}
fclose(fOut);
fclose(fIn);
E_QM_Min = E_MM_Min = 1.0E100;
for(i=0; i<nScan; i++) {
if(E_QM_Min > E_QM_Scaned[i]) {
E_QM_Min = E_QM_Scaned[i];
}
if(E_MM_Min > E_MM_Scaned[i]) {
E_MM_Min = E_MM_Scaned[i];
}
}
for(i=0; i<nScan; i++) {
E_QM_Scaned[i] = (E_QM_Scaned[i]-E_QM_Min)*HARTREE_To_KCAL;
E_MM_Scaned[i] -= E_MM_Min;
E_QM_MM_Diff[i] = E_QM_Scaned[i]-E_MM_Scaned[i];
if(E_MM_Scaned[i] > 60.0) { // an unusual large MM energy
w_Point[i] = 0.0;
}
else {
w_Point[i] = 1.0;
}
}
printf(" There are %d conformers\n", nScan );
for(i=0;i<nScan;i++) {
printf("%5d %8.3f %8.3f %8.3f %8.3f %d\n", i, Phi_Scaned[i], E_QM_Scaned[i], E_MM_Scaned[i], E_QM_MM_Diff[i], w_Point[i]==1.0 );
}
/*
sprintf(szName, "qm-mm-diff-%d.dat", Idx+1);
fOut = fopen(szName, "w");
for(i=0; i<nScan; i++) {
E_QM_Scaned[i] = (E_QM_Scaned[i]-E_QM_Min)*HARTREE_To_KCAL;
E_MM_Scaned[i] -= E_MM_Min;
fprintf(fOut, "%.1lf %.6lf %.6lf\n", Phi_Scaned[i], E_QM_Scaned[i], E_QM_Scaned[i]-E_MM_Scaned[i]);
// fprintf(fOut, "%.1lf %.12e %.6lf %.6lf\n", Phi_Scaned[i], E_QM_Scaned[i]);
// fprintf(fOut, "%.1lf %.6lf %.6lf %.6lf\n", Phi_Scaned[i], E_QM_Scaned[i], E_MM_Scaned[i], E_QM_Scaned[i] - E_MM_Scaned[i]);
}
fclose(fOut);
*/
memcpy(Mol_ESP.Para_k_Dih[IdxDihSelect[Idx]]+1, Para_k_Dih_Save, sizeof(double)*6);
memcpy(Mol_ESP.Para_phi[IdxDihSelect[Idx]]+1, Para_phi_Dih_Save, sizeof(double)*6);
}
void Add_Tip3_Rtf_File(void)
{
FILE *fOut, *fIn;
char ErrorMsg[256], szLine[256], *ReadLine, szBuff[256], szComment[256];
int ReadItem;
double net_cg_local=0.0;
szTxt_Rtf[0] = 0;
fIn = fopen(szRtfFile, "r");
if(fIn == NULL) {
sprintf(ErrorMsg, "Error in open file: %s\nQuit\n", szRtfFile);
Quit_With_Error_Msg(ErrorMsg);
}
else {
while(1) {
if(feof(fIn)) {
break;
}
ReadLine = fgets(szLine, 256, fIn);
if(ReadLine == NULL) {
break;
}
else {
if(strncmp(szLine,"RESI", 4)==0) {
ReadItem = sscanf(szLine, "%s%s%lf", szBuff, szBuff, &net_cg_local);
if(ReadItem == 3) {
if(fabs(net_cg_local-net_charge) > 1.0E-1) {
Quit_With_Error_Msg("The charge in rtf is NOT consistent with the charge provided by user.\nQuit\n");
}
Extract_Comment(szLine, szComment);
sprintf(szLine, "RESI MOL %6.3lf %s", net_cg_local, szComment);
}
else {
ReadItem = sscanf(szLine, "%s%lf", szBuff, &net_cg_local);
if(ReadItem == 2) {
if(fabs(net_cg_local-net_charge) > 1.0E-1) {
Quit_With_Error_Msg("The charge in rtf is NOT consistent with the charge provided by user.\nQuit\n");
}
Extract_Comment(szLine, szComment);
sprintf(szLine, "RESI MOL %6.3lf %s", net_cg_local, szComment);
}
}
}
if(strncmp(szLine, "END", 3)==0) {
continue;
}
else if(strncmp(szLine, "ANGL", 4)==0) {
continue;
}
else if(strncmp(szLine, "DIHE", 4)==0) {
continue;
}
strcat(szTxt_Rtf, szLine);
}
}
fclose(fIn);
}
fOut = fopen(szRtfFile, "w");
fprintf(fOut, "%s", szTxt_Rtf);
fprintf(fOut, "\n\nMASS 101 HT_W 1.008000 H ! TIPS3P WATER HYDROGEN\n");
fprintf(fOut, "MASS 102 OT_W 15.999400 O ! TIPS3P WATER OXYGEN\n\n");
fprintf(fOut, "RESI TIP3 0.000 ! tip3p water model, generate using noangle nodihedral\n");
fprintf(fOut, "GROUP\nATOM OH2 OT_W -0.834\nATOM H1 HT_W 0.417\nATOM H2 HT_W 0.417\nBOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake\nANGLE H1 OH2 H2 ! required\n");
fprintf(fOut, "\n\nEND\n");
fclose(fOut);
}
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], *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;
}
void CWORKER::Start_Job(int CoreNum, int ID, char szGjf[], char szOut[])
{
char szCmd[256], szEnv[256], szErrorMsg[256];
FILE *fIn;
nCore = CoreNum;
Status = BUSY;
JobID = ID;
strcpy(szInput, szGjf);
strcpy(szOutput, szOut);
sprintf(szEnv, "%s/%d", szGAUSS_SCRDIR_Base, ID);
#ifdef WIN32
if( SetEnvironmentVariable(szGAUSS_SCRDIR, szEnv) == 0) {
#else
if (setenv(szGAUSS_SCRDIR, szEnv, 1) < 0) {
#endif
sprintf(szErrorMsg, "Error setting env for %s with ID = %d.\n", szGAUSS_SCRDIR, ID);
Quit_With_Error_Msg(szErrorMsg);
}
sprintf(szCmd, "mkdir %s", szEnv);
system(szCmd);
Update_Core_Number_Input_File();
sprintf(szCmd, "%s < %s > %s &", szExe_G09, szInput, szOutput);
fIn = fopen(szOutput, "r");
if(fIn == NULL) {
system(szCmd);
}
else {
fclose(fIn);
Get_Job_Status();
}
}
#define SIZE_CHECK (512)
int CWORKER::Get_Job_Status(void)
{
FILE *fIn;
char szErrorMsg[256], szBuff[1024];
int i, nLen;
if(Status == IDLE) {
return Status;
}
fIn = fopen(szOutput, "rb");
if(fIn == NULL) {
sprintf(szErrorMsg, "Error in open file %s for reading.\nQuit\n", szOutput);
Quit_With_Error_Msg(szErrorMsg);
}
fseek(fIn, -SIZE_CHECK, SEEK_END);
nLen = fread(szBuff, 1, SIZE_CHECK, fIn);
for(i=0; i<nLen; i++) {
if(strncmp(szBuff+i, "Job cpu time:", 13) == 0) {
fclose(fIn);
JobStatus[JobID] = Job_Done;
Status = IDLE;
nJobDone++;
return Status;
}
}
fclose(fIn);
Status = BUSY;
return Status;
}
void Setup_QM_Level(void)
{
FILE *fIn;
char *ReadLine, szLine[256], szSubStr_1[256], szSubStr_2[256], ErrorMsg[256];
char szKey_QM_MEM[256], szKey_QM_NPROC[256], szQM_Level_Opt[256], szQM_Level_Dimer_Opt[256], szQM_Level_ESP[256], szQM_Level_E_Monomer[256], szQM_Level_1D_Scan[256];
int nStr, KeyCount;
fIn = fopen(szQMParaFile, "r");
if(fIn == NULL) {
sprintf(ErrorMsg, "Fail to open file %s\nQuit\n", szQMParaFile);
Quit_With_Error_Msg(ErrorMsg);
}
KeyCount = 0;
while(1) {
if(feof(fIn)) {
break;
}
ReadLine = fgets(szLine, 256, fIn);
Replace_NewLine(szLine);
if(ReadLine == NULL) {
break;
}
else {
nStr = Split_Into_Two_String(szLine, szSubStr_1, szSubStr_2);
if(nStr == 2) {
if(strcmp(szSubStr_1,"QM_MEM")==0) {
strcpy(szKey_QM_MEM, szSubStr_2);
KeyCount++;
}
else if(strcmp(szSubStr_1,"QM_NPROC")==0) {
strcpy(szKey_QM_NPROC, szSubStr_2);
KeyCount++;
nCore_Per_Node = atoi(szKey_QM_NPROC);
}
else if(strcmp(szSubStr_1,"QM_LEVEL_OPT")==0) {
strcpy(szQM_Level_Opt, szSubStr_2);
KeyCount++;
}
else if(strcmp(szSubStr_1,"QM_LEVEL_DIMER_OPT")==0) {
strcpy(szQM_Level_Dimer_Opt, szSubStr_2);
KeyCount++;
}
else if(strcmp(szSubStr_1,"QM_LEVEL_ESP")==0) {
strcpy(szQM_Level_ESP, szSubStr_2);
KeyCount++;
}
else if(strcmp(szSubStr_1,"QM_LEVEL_E_MONOMER")==0) {
strcpy(szQM_Level_E_Monomer, szSubStr_2);
KeyCount++;
}
else if(strcmp(szSubStr_1,"QM_LEVEL_1D_SCAN")==0) {
strcpy(szQM_Level_1D_Scan, szSubStr_2);
KeyCount++;
}
}
}
}
fclose(fIn);
Determine_QM_Level(szQM_Level_1D_Scan);
if(KeyCount != 7) { // !!!
sprintf(ErrorMsg, "Setup_QM_Level> Error: incomplete entries in %s\nQuit\n", szQMParaFile);
Quit_With_Error_Msg(ErrorMsg);
}
sprintf(szQM_Level_1D_Scan_Cmd, "%%mem=%s%%nproc=%s%sMol dihedral scan\n\n%d,1\n",
szKey_QM_MEM, szKey_QM_NPROC, szQM_Level_1D_Scan, netcharge_mol);
// printf("%s", szQM_Level_1D_Scan_Cmd);
}
