double Geo_Constraint_Bond(unsigned n, const double *x, double *grad, void *data)
{
int ia, ib, iPos;
double r, r0, g[2][3];
CMol* pMol;
GEO_FIX_BOND *Geo_Fix_r;
Geo_Fix_r = (GEO_FIX_BOND*)data;
pMol = (CMol*)(Geo_Fix_r->pMol);
ia = Geo_Fix_r->ia;
ib = Geo_Fix_r->ib;
r0 = Geo_Fix_r->r0;
if(grad) {
r = pMol->Query_Distance(ia, ib, 1, g);
memset(grad, 0, sizeof(double)*n);
iPos = 3 * ia;
grad[iPos ] = g[0][0];
grad[iPos+1] = g[0][1];
grad[iPos+2] = g[0][2];
iPos = 3 * ib;
grad[iPos ] = g[1][0];
grad[iPos+1] = g[1][1];
grad[iPos+2] = g[1][2];
}
else {
r = pMol->Query_Distance(ia, ib, 0, g);
}
return (r - r0);
}
void Get_Representative_14_Atoms(int iDih)
{
int ia, ib, ic, id, i, Idx, nAtom_Connected, nAtom_Connected_Max=0;
ib = Dih_Bond[iDih][1];
ic = Dih_Bond[iDih][2];
//start to find the representative atom for the left side, ia
nAtom_Connected_Max=-100;
ia = -1;
for(i=0; i<Bond_Count[ib]; i++) {
Idx = Bond_List[ib][i];
if(Idx == ic) {
continue;
}
nAtom_Connected = Mol.Count_All_Atoms_Connected(Idx, ib);
if(nAtom_Connected > nAtom_Connected_Max) {
nAtom_Connected_Max = nAtom_Connected;
ia = Idx;
}
else if( (i!=0) && (nAtom_Connected == nAtom_Connected_Max) && (Mol.mass[Idx] > Mol.mass[ia]) ) {
ia = Idx;
}
}
if(ia>=0) {
Dih_Bond[iDih][0] = ia;
}
else {
Quit_With_Error_Msg("Fail to find the representative atom (heavy atom), ia, in dihedral.\nQuit\n");
}
//end to find the representative atom for the left side, ia
//start to find the representative atom for the left side, ia
nAtom_Connected_Max=-100;
id = -1;
for(i=0; i<Bond_Count[ic]; i++) {
Idx = Bond_List[ic][i];
if(Idx == ib) {
continue;
}
nAtom_Connected = Mol.Count_All_Atoms_Connected(Idx, ic);
if(nAtom_Connected > nAtom_Connected_Max) {
nAtom_Connected_Max = nAtom_Connected;
id = Idx;
}
else if( (i!=0) && (nAtom_Connected == nAtom_Connected_Max) && (Mol.mass[Idx] > Mol.mass[id]) ) {
id = Idx;
}
}
if(id>=0) {
Dih_Bond[iDih][3] = id;
}
else {
Quit_With_Error_Msg("Fail to find the representative atom (heavy atom), id, in dihedral.\nQuit\n");
}
//end to find the representative atom for the left side, ia
return;
}
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 To_Setup_All_Dihedral_Constraint(void)
{
int i;
Mol_ESP.nPhi_Fixed = 0;
for(i=0; i<n_Phi; i++) {
Mol_ESP.To_Fix_Dihedral(DihList[i][0], DihList[i][1], DihList[i][2], DihList[i][3],
Mol_ESP.Query_Dihedral(DihList[i][0], DihList[i][1], DihList[i][2], DihList[i][3], 0, NULL));
}
}
double Geo_Constraint_Dihedral(unsigned n, const double *x, double *grad, void *data)
{
int ia, ib, ic, id, iPos;
double phi, phi0, d_phi, g[4][3];
CMol* pMol;
GEO_FIX_DIHEDRAL *Geo_Fix_phi;
Geo_Fix_phi = (GEO_FIX_DIHEDRAL*)data;
pMol = (CMol*)(Geo_Fix_phi->pMol);
ia = Geo_Fix_phi->ia;
ib = Geo_Fix_phi->ib;
ic = Geo_Fix_phi->ic;
id = Geo_Fix_phi->id;
phi0 = Geo_Fix_phi->phi0;
if(grad) {
phi = pMol->Query_Dihedral(ia, ib, ic, id, 1, g);
memset(grad, 0, sizeof(double)*n);
iPos = 3 * ia;
grad[iPos ] = g[0][0];
grad[iPos+1] = g[0][1];
grad[iPos+2] = g[0][2];
iPos = 3 * ib;
grad[iPos ] = g[1][0];
grad[iPos+1] = g[1][1];
grad[iPos+2] = g[1][2];
iPos = 3 * ic;
grad[iPos ] = g[2][0];
grad[iPos+1] = g[2][1];
grad[iPos+2] = g[2][2];
iPos = 3 * id;
grad[iPos ] = g[3][0];
grad[iPos+1] = g[3][1];
grad[iPos+2] = g[3][2];
}
else {
phi = pMol->Query_Dihedral(ia, ib, ic, id, 0, g);
}
d_phi = phi - phi0;
if(d_phi < -PI) {
d_phi += PI2;
}
else if(d_phi > PI) {
d_phi -= PI2;
}
return d_phi;
}
void Gen_Soft_Dihedral_List_MD_High_T(void)
{
int Step, Idx, RecIdx, iPos, ia, ib, ic, id;
Mol.Init_LangevinDynamics(T_Sim);
nDihedral = Mol.nDihedral;
for(Step=1; Step<=MAX_STEP; Step++) {
Mol.LangevinDynamics(Step);
if(Step%GAP==0) {
RecIdx = Step/GAP - 1;
for(Idx=0; Idx<nDihedral; Idx++) {
dih_List[RecIdx][Idx] = Mol.dih_Phi_List[Idx];
}
}
}
Cal_Sig();
Cal_Sig_Shift_PI2();
n_Soft_Dih = 0;
for(Idx=0; Idx<nDihedral; Idx++) {
if(IsRigidDih[Idx] == 0) {
iPos = Idx*4;
ia = Mol.DihedralList[iPos ];
ib = Mol.DihedralList[iPos+1];
ic = Mol.DihedralList[iPos+2];
id = Mol.DihedralList[iPos+3];
if(ib <= ic) {
if(!Is_In_Soft_Dihedral_List(ib, ic)) {
Dih_Bond[n_Soft_Dih][0] = ia;
Dih_Bond[n_Soft_Dih][1] = ib;
Dih_Bond[n_Soft_Dih][2] = ic;
Dih_Bond[n_Soft_Dih][3] = id;
n_Soft_Dih++;
printf("%3d %3d %3d %3d \n", Mol.DihedralList[iPos]+1, Mol.DihedralList[iPos+1]+1, Mol.DihedralList[iPos+2]+1, Mol.DihedralList[iPos+3]+1);
}
}
else {
if(!Is_In_Soft_Dihedral_List(ic, ib)) {
Dih_Bond[n_Soft_Dih][0] = id;
Dih_Bond[n_Soft_Dih][1] = ic;
Dih_Bond[n_Soft_Dih][2] = ib;
Dih_Bond[n_Soft_Dih][3] = ia;
n_Soft_Dih++;
printf("%3d %3d %3d %3d \n", Mol.DihedralList[iPos]+1, Mol.DihedralList[iPos+1]+1, Mol.DihedralList[iPos+2]+1, Mol.DihedralList[iPos+3]+1);
}
}
}
}
}
int Read_Soft_DihedralList(void)
{
FILE *fIn;
int ReadItem;
char szLine[256], *ReadLine;
n_Phi = 0;
fIn = fopen(szPhiToScan, "r");
while(1) {
if(feof(fIn)) {
break;
}
ReadLine = fgets(szLine, 128, fIn);
if(ReadLine == NULL) {
break;
}
ReadItem = sscanf(szLine, "%d %d %d %d %lf %lf %lf %lf %lf %lf",
&(DihList[n_Phi][0]), &(DihList[n_Phi][1]), &(DihList[n_Phi][2]), &(DihList[n_Phi][3]),
&(Phi_Set[n_Phi][0]), &(Phi_Set[n_Phi][1]), &(Phi_Set[n_Phi][2]), &(Phi_Set[n_Phi][3]), &(Phi_Set[n_Phi][4]), &(Phi_Set[n_Phi][5]));
if(ReadItem > 4) {
DihList[n_Phi][0]--;
DihList[n_Phi][1]--;
DihList[n_Phi][2]--;
DihList[n_Phi][3]--;
IdxDihSelect[n_Phi] = Mol.Query_Dihedral_Index(DihList[n_Phi][0], DihList[n_Phi][1], DihList[n_Phi][2], DihList[n_Phi][3]);
if(IdxDihSelect[n_Phi] < 0) {
Quit_With_Error_Msg("Fail to identify the index of one soft dihedral.\n");
}
Mol.BuildSegmentList_Dihedrals(IdxDihSelect[n_Phi]);
n_State_List[n_Phi] = ReadItem - 4;
n_Phi++;
}
else {
break;
}
}
fclose(fIn);
memcpy(Phi_Set_Save, Phi_Set, sizeof(double)*N_MAX_DIH*MAX_N_STATE);
memcpy(n_State_List_Save, n_State_List, sizeof(int)*N_MAX_DIH);
return n_Phi;
}
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 Cal_E_MM_Scaned(void)
{
int i, j, nAtom, Count=0;
double E_Min_Local_QM;
E_Scan_MM_Mean = 0.0;
E_Scan_QM_Mean = 0.0;
nAtom = Mol_ESP.nAtom;
for(i=0; i<n_Phi; i++) {
E_Min_Local_QM = 1.0E100;
for(j=0; j<nScan_List[i]; j++) {
if(E_Scan_QM[i][j] < E_Min_Local_QM) { // to find the lowest QM energy
E_Min_Local_QM = E_Scan_QM[i][j];
}
}
for(j=0; j<nScan_List[i]; j++) {
memcpy(Mol_ESP.x, x_Scan_list[i][j], sizeof(double)*nAtom);
memcpy(Mol_ESP.y, y_Scan_list[i][j], sizeof(double)*nAtom);
memcpy(Mol_ESP.z, z_Scan_list[i][j], sizeof(double)*nAtom);
E_Scan_MM[i][j] = Mol_ESP.Cal_E(0);
if( E_Scan_QM[i][j] < (E_Min_Local_QM+6.0) ) { // skip configuration with much higher energies
E_Scan_QM_Mean += E_Scan_QM[i][j];
E_Scan_MM_Mean += E_Scan_MM[i][j];
Count ++;
}
}
}
E_Scan_QM_Mean /= Count;
E_Scan_MM_Mean /= Count;
}
int main(int argc, char *argv[])
{
if(argc < 4) {
printf("Usage: add-tip3 your-rtf your-prm your-psf E14FAC\nQuit\n");
return 1;
}
strcpy(szRtfFile, argv[1]);
strcpy(szPrmFile, argv[2]);
strcpy(szXpsfName, argv[3]);
if(argc == 5) {
E14FAC = atof(argv[4]);
}
fFile_Run_Log = fopen("log-modify-rtf.txt", "w");
Mol.ReadPSF(szXpsfName, 0);
GetAtomTypeFromMass();
Count_Bond_and_H();
Assign_Alpha_Miller();
Add_Tip3_Rtf_File();
Add_Tip3_Prm_File();
fclose(fFile_Run_Log);
return 0;
}
int main(int argc, char *argv[])
{
if(argc == 2) {
To_Exclude_Methyl_Torsion = 0;
}
else {
To_Exclude_Methyl_Torsion = 1;
}
memset(IsRigidDih, 0, sizeof(int)*MAX_DIHEDRAL_LIST);
fFile_Run_Log = fopen("identify-soft.log", "w");
ForceField.ReadForceField(szForceFiled);
Mol.ReadPSF(szXpsfFile, 0);
Mol.AssignForceFieldParameters(&ForceField);
Mol.ReadCRD(szCrdFile);
Setup_Bond_List();
// Gen_Soft_Dihedral_List_MD_High_T();
// printf("\n\n");
Gen_Soft_Dihedral_List_Excluding_Ring();
printf("\n\n");
To_Refine_Soft_Dihedral_List();
/*
fData = fopen("dihedral.txt", "w");
for(Step=0; Step<MAX_STEP/GAP; Step++) {
fprintf(fData, "%8d ", Step);
for(Idx=0; Idx<nDihedral; Idx++) {
if(IsRigidDih[Idx] == 0) {
fprintf(fData, " %7.2lf", dih_List[Step][Idx]);
}
}
fprintf(fData, "\n");
}
fclose(fData);
*/
fclose(fFile_Run_Log);
return 0;
}
int Read_Soft_DihedralList(void)
{
FILE *fIn;
int ReadItem;
char szLine[256], *ReadLine, ErrorMsg[256], szFlag[256];
n_Phi = 0;
fIn = fopen(szPhiToScan, "r");
while(1) {
if(feof(fIn)) {
sprintf(ErrorMsg, "Fail to open file: %s\nQuit\n", szPhiToScan);
Quit_With_Error_Msg(ErrorMsg);
}
ReadLine = fgets(szLine, 128, fIn);
if(ReadLine == NULL) {
break;
}
ReadItem = sscanf(szLine, "%d %d %d %d %s",
&(DihList[n_Phi][0]), &(DihList[n_Phi][1]), &(DihList[n_Phi][2]), &(DihList[n_Phi][3]), szFlag);
if(ReadItem >= 4) {
DihList[n_Phi][0]--;
DihList[n_Phi][1]--;
DihList[n_Phi][2]--;
DihList[n_Phi][3]--;
IdxDihSelect[n_Phi] = Mol_ESP.Query_Dihedral_Index(DihList[n_Phi][0], DihList[n_Phi][1], DihList[n_Phi][2], DihList[n_Phi][3]);
if(IdxDihSelect[n_Phi] < 0) {
Quit_With_Error_Msg("Fail to identify the index of one soft dihedral.\n");
}
Is_Dih_Fixed[n_Phi] = 0;
if(ReadItem==5) {
if( (strcmp(szFlag, "F")==0) || (strcmp(szFlag, "f")==0) ) {
Is_Dih_Fixed[n_Phi] = 1;
}
}
n_Phi++;
}
else {
break;
}
}
fclose(fIn);
Setup_Phi_Constraint_List();
return n_Phi;
}
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;
}
double func_Geo_Opt_Constraint(unsigned n, const double *x, double *grad, void *my_func_data)
{
int i, iPos, nAtom;
double E_Total, *gx, *gy, *gz, *xx, *yy, *zz;
CMol* pMol;
pMol = (CMol*)my_func_data;
nAtom = pMol->nAtom;
gx = pMol->grad_x;
gy = pMol->grad_y;
gz = pMol->grad_z;
xx = pMol->x;
yy = pMol->y;
zz = pMol->z;
if(grad) {
Iter_Opt_Constrained ++;
for(i=0; i<nAtom; i++) { // update the coordinate
iPos = 3*i;
xx[i] = x[iPos ];
yy[i] = x[iPos+1];
zz[i] = x[iPos+2];
}
E_Total = pMol->Cal_E(0);
for(i=0; i<nAtom; i++) { // get the gradient
iPos = 3*i;
grad[iPos ] = gx[i];
grad[iPos+1] = gy[i];
grad[iPos+2] = gz[i];
}
}
else {
E_Total = pMol->Cal_E(0);
}
// printf( "TT: %f\n", E_Total );
return E_Total;
}
double Geo_Constraint_Angle(unsigned n, const double *x, double *grad, void *data)
{
int ia, ib, ic, iPos;
double theta, theta0, g[3][3];
CMol* pMol;
GEO_FIX_ANGLE *Geo_Fix_theta;
Geo_Fix_theta = (GEO_FIX_ANGLE*)data;
pMol = (CMol*)(Geo_Fix_theta->pMol);
ia = Geo_Fix_theta->ia;
ib = Geo_Fix_theta->ib;
ic = Geo_Fix_theta->ic;
theta0 = Geo_Fix_theta->theta0;
if(grad) {
theta = pMol->Query_Angle(ia, ib, ic, 1, g);
memset(grad, 0, sizeof(double)*n);
iPos = 3 * ia;
grad[iPos ] = g[0][0];
grad[iPos+1] = g[0][1];
grad[iPos+2] = g[0][2];
iPos = 3 * ib;
grad[iPos ] = g[1][0];
grad[iPos+1] = g[1][1];
grad[iPos+2] = g[1][2];
iPos = 3 * ic;
grad[iPos ] = g[2][0];
grad[iPos+1] = g[2][1];
grad[iPos+2] = g[2][2];
}
else {
theta = pMol->Query_Angle(ia, ib, ic, 0, g);
}
return (theta - theta0);
}
int main(int argc, char **argv)
{
int i;
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);
}
ForceField.ReadForceField("org-mol.prm");
// ForceField.ReadForceField("mol.prm");
Mol_ESP.ReadPSF("org-mol.xpsf", 0);
// Mol_ESP.ReadPSF("mol.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;
// i = 3;
for(i=0; i<n_Phi; i++) {
Cal_E_MM_QM_Diff(i);
Fit_Torsion_Parameters(i);
}
fflush(fFile_Run_Log);
fclose(fFile_Run_Log);
return 0;
}
int Read_Soft_DihedralList(void)
{
FILE *fIn;
int ReadItem;
char szLine[256], *ReadLine;
n_Phi = 0;
fIn = fopen(szPhiToScan, "r");
while(1) {
if(feof(fIn)) {
break;
}
ReadLine = fgets(szLine, 128, fIn);
if(ReadLine == NULL) {
break;
}
ReadItem = sscanf(szLine, "%d %d %d %d",
&(DihList[n_Phi][0]), &(DihList[n_Phi][1]), &(DihList[n_Phi][2]), &(DihList[n_Phi][3]));
if(ReadItem == 4) {
DihList[n_Phi][0]--;
DihList[n_Phi][1]--;
DihList[n_Phi][2]--;
DihList[n_Phi][3]--;
IdxDihSelect[n_Phi] = Mol_ESP.Query_Dihedral_Index(DihList[n_Phi][0], DihList[n_Phi][1], DihList[n_Phi][2], DihList[n_Phi][3]);
if(IdxDihSelect[n_Phi] < 0) {
Quit_With_Error_Msg("Fail to identify the index of one soft dihedral.\n");
}
n_Phi++;
}
else {
break;
}
}
fclose(fIn);
Setup_Phi_Constraint_List();
return n_Phi;
}
void Output_1D_QM_MM(void)
{
FILE *fOut;
char szName[256];
int i, j, nAtom;
double E_Min_1D_QM, E_Min_1D_MM_Mean, E_Min_1D_QM_Mean, E_Min_1D_QM_MM_Shift, Weight_Sum;
if(ProgID != 0) {
return;
}
nAtom = Mol_ESP.nAtom;
for(i=0; i<n_Phi; i++) {
sprintf(szName, "1d-qm-mm-%d.dat", i+1);
fOut = fopen(szName, "w");
E_Min_1D_QM = 1.0E100;
for(j=0; j<nScan_List[i]; j++) {
memcpy(Mol_ESP.x, x_Scan_list[i][j], sizeof(double)*nAtom);
memcpy(Mol_ESP.y, y_Scan_list[i][j], sizeof(double)*nAtom);
memcpy(Mol_ESP.z, z_Scan_list[i][j], sizeof(double)*nAtom);
E_Scan_MM[i][j] = Mol_ESP.Cal_E(0);
if(E_Min_1D_QM > E_Scan_QM[i][j]) {
E_Min_1D_QM = E_Scan_QM[i][j];
}
}
E_Min_1D_MM_Mean = E_Min_1D_QM_Mean = 0.0;
Weight_Sum = 0.0;
for(j=0; j<nScan_List[i]; j++) {
Weight_Sum += w_Scan_List[i][j];
E_Min_1D_MM_Mean += (w_Scan_List[i][j] * E_Scan_MM[i][j] );
E_Min_1D_QM_Mean += (w_Scan_List[i][j] * E_Scan_QM[i][j] );
}
E_Min_1D_QM_MM_Shift = (E_Min_1D_QM_Mean - E_Min_1D_MM_Mean)/Weight_Sum;
for(j=0; j<nScan_List[i]; j++) {
fprintf(fOut, "%.1lf %.5lf %.5lf\n", Phi_Scan_List[i][j], E_Scan_QM[i][j]-E_Min_1D_QM, E_Scan_MM[i][j]+E_Min_1D_QM_MM_Shift-E_Min_1D_QM); // the relative 1D energy
}
fclose(fOut);
}
}
void Gen_Soft_Dihedral_List_Excluding_Ring(void)
{
int i, nDih, iPos, ia, ib, ic, id;
nDih = Mol.nDihedral;
n_Soft_Dih = 0;
for(i=0; i<nDih; i++) {
if(Mol.Is_A_Dihedrals_In_A_Ring(i) == 0) {
iPos = i*4;
ia = Mol.DihedralList[iPos ];
ib = Mol.DihedralList[iPos+1];
ic = Mol.DihedralList[iPos+2];
id = Mol.DihedralList[iPos+3];
if(ib <= ic) {
if(!Is_In_Soft_Dihedral_List(ib, ic)) {
Dih_Bond[n_Soft_Dih][0] = ia;
Dih_Bond[n_Soft_Dih][1] = ib;
Dih_Bond[n_Soft_Dih][2] = ic;
Dih_Bond[n_Soft_Dih][3] = id;
n_Soft_Dih++;
printf("%3d %3d %3d %3d \n", Mol.DihedralList[iPos]+1, Mol.DihedralList[iPos+1]+1, Mol.DihedralList[iPos+2]+1, Mol.DihedralList[iPos+3]+1);
}
}
else {
if(!Is_In_Soft_Dihedral_List(ic, ib)) {
Dih_Bond[n_Soft_Dih][0] = id;
Dih_Bond[n_Soft_Dih][1] = ic;
Dih_Bond[n_Soft_Dih][2] = ib;
Dih_Bond[n_Soft_Dih][3] = ia;
n_Soft_Dih++;
printf("%3d %3d %3d %3d \n", Mol.DihedralList[iPos]+1, Mol.DihedralList[iPos+1]+1, Mol.DihedralList[iPos+2]+1, Mol.DihedralList[iPos+3]+1);
}
}
}
}
}
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;
}
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 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);
}
double CalObjectiveFunction(double Para_List[], int Get_E_Rotamer)
{
int i, j, nAtom, time_1, time_2;
double d_E, E_Shift, w_1D;
double Chi_SQ_Rotamer_Local;
double E_Rotamer_MM_Local[MAX_ROTAMER];
double E_Min_1D_MM_Mean, E_Min_1D_QM_Mean, E_Min_1D_QM_MM_Shift, Weight_Sum;
Chi_SQ = Chi_SQ_1D = Chi_SQ_Rotamer = 0.0;
Chi_SQ_Rotamer_Local = 0.0;
w_1D = 1.0 - w_Rotamer;
time_1 = time(NULL);
Distribute_Torsion_Parameters();
Assign_Torsion_Parameters();
E_Shift = Para_List[10*n_Phi];
nAtom = Mol_ESP.nAtom;
for(i=0; i<n_Phi; i++) {
for(j=0; j<nScan_List[i]; j++) {
memcpy(Mol_ESP.x, x_Scan_list[i][j], sizeof(double)*nAtom);
memcpy(Mol_ESP.y, y_Scan_list[i][j], sizeof(double)*nAtom);
memcpy(Mol_ESP.z, z_Scan_list[i][j], sizeof(double)*nAtom);
E_Scan_MM[i][j] = Mol_ESP.Cal_E(0);
}
E_Min_1D_MM_Mean = E_Min_1D_QM_Mean = 0.0;
Weight_Sum = 0.0;
for(j=0; j<nScan_List[i]; j++) {
Weight_Sum += w_Scan_List[i][j];
E_Min_1D_MM_Mean += (w_Scan_List[i][j] * E_Scan_MM[i][j] );
E_Min_1D_QM_Mean += (w_Scan_List[i][j] * E_Scan_QM[i][j] );
}
E_Min_1D_QM_MM_Shift = (E_Min_1D_QM_Mean - E_Min_1D_MM_Mean)/Weight_Sum;
for(j=0; j<nScan_List[i]; j++) {
d_E = (E_Scan_QM[i][j] - E_Scan_MM[i][j] - E_Min_1D_QM_MM_Shift); // fit the relative 1D energy profile
Chi_SQ_1D += (d_E*d_E*w_Scan_List[i][j]);
}
}
Chi_SQ_1D *= (w_1D/w_Scan_Sum);
for(i=0; i<nRotamer; i++) {
E_Rotamer_MM[i] = E_Rotamer_MM_Local[i] = 0.0;
if(i%nProc != ProgID) { //only proceed when i%nProc == ProgID, do job decomposition
continue;
}
memcpy(Mol_ESP.x, x_Rotamer_Opt[i], sizeof(double)*nAtom);
memcpy(Mol_ESP.y, y_Rotamer_Opt[i], sizeof(double)*nAtom);
memcpy(Mol_ESP.z, z_Rotamer_Opt[i], sizeof(double)*nAtom);
Mol_ESP.FullGeometryOptimization_LBFGS_step(1);
E_Rotamer_MM_Local[i] = Mol_ESP.Cal_E(0);
d_E = E_Rotamer_QM[i] - E_Rotamer_MM_Local[i] - E_Shift;
Chi_SQ_Rotamer_Local += (d_E*d_E*w_rotamer_List[i]);
}
if(Get_E_Rotamer) {
//eliot (from Matt Harvey)
for( int i = 0 ; i < nRotamer; i++ ) { E_Rotamer_MM[i] += E_Rotamer_MM_Local[i]; }
Chi_SQ_Rotamer = Chi_SQ_Rotamer_Local;
//eliot MPI_Allreduce(E_Rotamer_MM_Local, E_Rotamer_MM, nRotamer, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
}
//eliot MPI_Allreduce(&Chi_SQ_Rotamer_Local, &Chi_SQ_Rotamer, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
// MPI_Bcast(&Chi_SQ_Rotamer, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
printf(" w_rotamer_Sum = %f\n", w_rotamer_Sum );
Chi_SQ_Rotamer *= (w_Rotamer/w_rotamer_Sum);
Chi_SQ = Chi_SQ_1D + Chi_SQ_Rotamer;
// MPI_Barrier(MPI_COMM_WORLD);
// printf("%lf\n", Chi_SQ);
// MPI_Finalize();
time_2 = time(NULL);
/*
if(ProgID == 0) {
FILE *fOut;
fOut = fopen("time-rec.txt", "a+");
fseek(fOut, 0, SEEK_END);
fprintf(fOut, "%d\n", time_2-time_1);
fclose(fOut);
}
*/
printf("Chi_SQ=%f\n", Chi_SQ );
return Chi_SQ;
}
double Geoometry_Optimization_With_Constraint(CMol *pMol)
{
return (pMol->Cal_E(0));
nlopt_opt opt, opt_AugLag;
int Return_Opt, nAtom, nDim, i, iPos;
double E_min, x[MAX_NUM_ATOM*3];
Mol_ESP.Restrain_All_Torsions(1); // apply soft restraints on all soft dihedrals
nAtom = pMol->nAtom;
nDim = 3 * nAtom;
printf("\nMM before:\t");
for(i=0; i<n_Phi; i++) {
printf("%3d %3d %3d %3d %8.4lf\n", DihList[i][0], DihList[i][1], DihList[i][2], DihList[i][3],
Mol_ESP.Query_Dihedral(DihList[i][0], DihList[i][1], DihList[i][2], DihList[i][3], 0, NULL));
}
double AUG_LAG_ICM_TOL = 1.0E-17;
opt_AugLag = nlopt_create(NLOPT_LD_LBFGS_GEO, nDim);
nlopt_set_min_objective(opt_AugLag, func_Geo_Opt_Constraint, pMol);
// pMol->SavePdb("opt-free.pdb");
for(i=0; i<pMol->nBond_Fixed; i++) {
int ret=0;
pMol->Geo_Fix_r0[i].pMol = pMol;
ret =nlopt_add_equality_constraint(opt_AugLag, Geo_Constraint_Bond, &(pMol->Geo_Fix_r0[i]), 2.0E-6);
printf(" Fixing bond %d\n", i );
}
for(i=0; i<pMol->nAngle_Fixed; i++) {
int ret=0;
pMol->Geo_Fix_theta0[i].pMol = pMol;
ret=nlopt_add_equality_constraint(opt_AugLag, Geo_Constraint_Angle, &(pMol->Geo_Fix_theta0[i]), 2.0E-6);
printf(" Fixing angle %d\n", i );
}
for(i=0; i<pMol->nPhi_Fixed; i++) {
int ret=0;
pMol->Geo_Fix_phi0[i].pMol = pMol;
ret=nlopt_add_equality_constraint(opt_AugLag, Geo_Constraint_Dihedral, &(pMol->Geo_Fix_phi0[i]), 2.0E-6);
printf(" Fixing phi %d : %d\n", i, ret );
}
nlopt_set_xtol_rel(opt_AugLag, 2E-7);
// opt = nlopt_create(NLOPT_LD_LBFGS_GEO, nDim);
// opt = nlopt_create(NLOPT_LN_COBYLA, nDim);
// nlopt_set_min_objective(opt, func_Geo_Opt_Constraint, pMol);
// nlopt_set_xtol_rel(opt, 1E-7);
// nlopt_set_local_optimizer(opt_AugLag, opt);
// nlopt_destroy(opt);
for(i=0; i<nAtom; i++) {
iPos = 3*i;
x[iPos ] = pMol->x[i];
x[iPos+1] = pMol->y[i];
x[iPos+2] = pMol->z[i];
}
Iter_Opt_Constrained = 0;
Return_Opt = nlopt_optimize(opt_AugLag, x, &E_min);
if (Return_Opt < 0) {
printf("nlopt failed : %d\n", Return_Opt);
}
// else {
// printf("After constrained optimization, E = %12.6lf\n", E_min);
// }
nlopt_destroy(opt_AugLag);
printf("MM after:\t");
for(i=0; i<n_Phi; i++) {
printf("%3d %3d %3d %3d %8.4lf\n", DihList[i][0], DihList[i][1], DihList[i][2], DihList[i][3],
Mol_ESP.Query_Dihedral(DihList[i][0], DihList[i][1], DihList[i][2], DihList[i][3], 0, NULL));
}
Mol_ESP.Restrain_All_Torsions(0); // lift soft restraints on all soft dihedrals
return (pMol->Cal_E(0));
}
int main(int argc, char **argv)
{
char ErrorMsg[256];
timebomb();
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);
//eliot 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();
if( nRotamer == 0 ) {
printf("No rotamers found. The should be at least one in all-rotamer.dat. Something has gone wrong in the previous step\n" );
exit(0);
}
Read_Tor_Para_1D_Fitting();
Assign_Torsion_Parameters();
Read_1D_Scan_QM_Data();
// Cal_E_MM_Scaned();
// Cal_E_MM_Rotamer();
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;
}
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;
}
