Commit: 49ce430526dbc569844bbb6c6f1c0d8a405d7a4d - MolDS (git)

Commit MetaInfo

• Révision: 49ce430526dbc569844bbb6c6f1c0d8a405d7a4d (tree)
• l'heure: 2011-09-29 23:19:16
• Auteur: Mikiya Fujii <mikiya.fujii@gmai...>
• Commiter: Mikiya Fujii

Message de Log

Input-parse-module for MD is added.

git-svn-id: https://svn.sourceforge.jp/svnroot/molds/MolDS/trunk@159 1136aad2-a195-0410-b898-f5ea1d11b9d8

Change Summary

• modified: src/base/InputParser.h
• modified: src/base/Parameters.h
• modified: src/input.in
• modified: src/zindo/ZindoS.h

Modification

--- a/src/base/InputParser.h
+++ b/src/base/InputParser.h
@@ -51,6 +51,11 @@ private:
    string messageCisNormTolerance;
    string messageCisMaxIterations;
    string messageCisMaxDimensions;
+   string messageMdConditions;
+   string messageMdTotalSteps;
+   string messageMdElecState;
+   string messageMdTimeWidth;
+   string messageFs;
    string stringYES;
    string stringNO;
    string stringSpace;
@@ -99,11 +104,18 @@ private:
    string stringCISMaxIter;
    string stringCISMaxDimensions;
    string stringCISNormTolerance;
+   string stringMD;
+   string stringMDEnd;
+   string stringMDTotalSteps;
+   string stringMDElecState;
+   string stringMDTimeWidth;
    void CalcMolecularBasics(Molecule* molecule);
    void CalcCisCondition(Molecule* molecule);
+   void CheckMdConditions();
    void OutputMolecularBasics(Molecule* molecule);
    void OutputScfConditions();
    void OutputCisConditions();
+   void OutputMdConditions();
    void OutputInputTerms(vector<string> inputTerms);
    bool IsCommentOut(string str);
    vector<string> GetInputTerms();
@@ -133,6 +145,11 @@ InputParser::InputParser(){
    this->messageCisNormTolerance = "\t\tNorm tolerance for the residual of the Davidson: ";
    this->messageCisMaxIterations = "\t\tMax iterations for the Davidson: ";
    this->messageCisMaxDimensions = "\t\tMax dimensions for the Davidson: ";
+   this->messageMdConditions = "\tMD conditions:\n";
+   this->messageMdTotalSteps = "\t\tTotal steps: ";
+   this->messageMdElecState = "\t\tElectronic eigen state: ";
+   this->messageMdTimeWidth = "\t\tTime width(dt): ";
+   this->messageFs = "[fs]";
    this->stringYES = "yes";
    this->stringNO = "no";
    this->stringSpace = " ";
@@ -181,6 +198,11 @@ InputParser::InputParser(){
    this->stringCISMaxIter = "max_iter";
    this->stringCISMaxDimensions = "max_dim";
    this->stringCISNormTolerance = "norm_tol";
+   this->stringMD = "md";
+   this->stringMDEnd = "md_end";
+   this->stringMDTotalSteps = "total_steps";
+   this->stringMDElecState = "electronic_state";
+   this->stringMDTimeWidth = "dt";
 }
 
 InputParser::~InputParser(){
@@ -462,6 +484,34 @@ void InputParser::Parse(Molecule* molecule){
          i = j;
       }
 
+      // MD condition
+      if(inputTerms[i].compare(this->stringMD) == 0){
+         Parameters::GetInstance()->SetRequiresMD(true);
+         int j=i+1;
+         while(inputTerms[j].compare(this->stringMDEnd) != 0){
+            // number of total steps 
+            if(inputTerms[j].compare(this->stringMDTotalSteps) == 0){
+               int totalSteps = atoi(inputTerms[j+1].c_str());
+               Parameters::GetInstance()->SetTotalStepsMD(totalSteps);
+               j++;
+            }
+            // index of electronic eigen state on whichi MD runs. 
+            if(inputTerms[j].compare(this->stringMDElecState) == 0){
+               int elecStateIndex = atoi(inputTerms[j+1].c_str());
+               Parameters::GetInstance()->SetElectronicStateIndexMD(elecStateIndex);
+               j++;
+            }
+            // time width for MD.
+            if(inputTerms[j].compare(this->stringMDTimeWidth) == 0){
+               double dt = atof(inputTerms[j+1].c_str()) * Parameters::GetInstance()->GetFs2AU();
+               Parameters::GetInstance()->SetTimeWidthMD(dt);
+               j++;
+            }
+            j++;   
+         }
+         i = j;
+      }
+
       // theory
       if(inputTerms[i].compare(this->stringTheory) == 0){
          int j=i+1;
@@ -514,6 +564,7 @@ void InputParser::Parse(Molecule* molecule){
    if(Parameters::GetInstance()->GetCurrentTheory() == ZINDOS){
       this->CalcCisCondition(molecule);
    }
+   this->CheckMdConditions();
 
    // output conditions
    this->OutputMolecularBasics(molecule);
@@ -521,6 +572,9 @@ void InputParser::Parse(Molecule* molecule){
    if(Parameters::GetInstance()->GetCurrentTheory() == ZINDOS){
       this->OutputCisConditions();
    }
+   if(Parameters::GetInstance()->RequiresMD()){
+      this->OutputMdConditions();
+   }
 
    // output inputs
    this->OutputInputTerms(inputTerms);
@@ -570,6 +624,13 @@ void InputParser::CalcCisCondition(Molecule* molecule){
    
 }
 
+void InputParser::CheckMdConditions(){
+   if(Parameters::GetInstance()->GetCurrentTheory() == ZINDOS){
+      int groundStateIndex = 0;
+      Parameters::GetInstance()->SetElectronicStateIndexMD(groundStateIndex);
+   }
+}
+
 void InputParser::OutputMolecularBasics(Molecule* molecule){
 
    molecule->OutputTotalNumberAtomsAOsValenceelectrons();
@@ -612,6 +673,16 @@ void InputParser::OutputCisConditions(){
    cout << "\n";
 }
 
+void InputParser::OutputMdConditions(){
+   cout << this->messageMdConditions;
+
+   printf("%s%d\n",this->messageMdElecState.c_str(),Parameters::GetInstance()->GetElectronicStateIndexMD());
+   printf("%s%d\n",this->messageMdTotalSteps.c_str(),Parameters::GetInstance()->GetTotalStepsMD());
+   printf("%s%lf%s\n",this->messageMdTimeWidth.c_str(),Parameters::GetInstance()->GetTimeWidthMD()/Parameters::GetInstance()->GetFs2AU(),this->messageFs.c_str());
+
+   cout << "\n";
+}
+
 void InputParser::OutputInputTerms(vector<string> inputTerms){
    
    // output input terms

--- a/src/base/Parameters.h
+++ b/src/base/Parameters.h
@@ -34,6 +34,7 @@ public:
    double GetKayser2AU();
    double GetGMolin2AU();
    double GetDegree2Radian();
+   double GetFs2AU();
    double GetBondingAdjustParameterK();
    TheoryType GetCurrentTheory();
    void SetCurrentTheory(TheoryType theory);
@@ -67,6 +68,14 @@ public:
    void SetMaxDimensionsCIS(int maxDimensionsCIS);
    double GetNormToleranceCIS();
    void SetNormToleranceCIS(double normToleranceCIS);
+   bool RequiresMD();
+   void SetRequiresMD(bool requiresMD);
+   int GetElectronicStateIndexMD();
+   void SetElectronicStateIndexMD(int electronicStateIndex);
+   int GetTotalStepsMD();
+   void SetTotalStepsMD(int totalSteps);
+   double GetTimeWidthMD();
+   void SetTimeWidthMD(double timeWidth);
 private:
    static Parameters* parameters;
    Parameters();
@@ -87,6 +96,7 @@ private:
    double kayser2AU;
    double gMolin2AU;
    double degree2Radian;
+   double fs2AU;
    double bondingAdjustParameterK; //see (3.79) in J. A. Pople book
    TheoryType currentTheory;
    double translatingDifference[3];
@@ -104,6 +114,10 @@ private:
    double normToleranceCIS;
    bool requiresCIS;
    bool isDavidsonCIS;
+   bool requiresMD;
+   int electronicStateIndexMD;
+   int totalStepsMD;
+   double timeWidthMD;
 };
 Parameters* Parameters::parameters = NULL;
 
@@ -141,6 +155,7 @@ void Parameters::SetDefaultValues(){
    this->eV2AU = 0.03674903;
    this->angstrom2AU = 1.0/0.5291772;
    this->kayser2AU = 4.556336*pow(10.0,-6.0);
+   this->fs2AU = 1.0/(2.418884326505*pow(10.0,-2.0));
    this->thresholdSCF = pow(10.0, -8.0);
    this->maxIterationsSCF = 100;
    this->dampingThreshSCF = 1.0;
@@ -171,6 +186,9 @@ void Parameters::SetDefaultValues(){
    this->maxIterationsCIS = 100;
    this->maxDimensionsCIS = 100;
    this->normToleranceCIS = pow(10.0, -6.0);
+   this->electronicStateIndexMD = 0;
+   this->totalStepsMD = 10;
+   this->timeWidthMD = 0.1*this->fs2AU;
 }
 
 double Parameters::GetThresholdSCF(){
@@ -249,6 +267,10 @@ double Parameters::GetDegree2Radian(){
    return this->degree2Radian;
 }
 
+double Parameters::GetFs2AU(){
+   return this->fs2AU;
+}
+
 double Parameters::GetBondingAdjustParameterK(){
    return this->bondingAdjustParameterK;
 }
@@ -402,6 +424,38 @@ void Parameters::SetNormToleranceCIS(double normToleranceCIS){
    this->normToleranceCIS = normToleranceCIS;
 }
 
+bool Parameters::RequiresMD(){
+   return this->requiresMD;
+}
+
+void Parameters::SetRequiresMD(bool requiresMD){
+   this->requiresMD = requiresMD;
+}
+
+int Parameters::GetElectronicStateIndexMD(){
+   return this->electronicStateIndexMD;
+}
+
+void Parameters::SetElectronicStateIndexMD(int electronicStateIndex){
+   this->electronicStateIndexMD = electronicStateIndex;
+}
+
+int Parameters::GetTotalStepsMD(){
+   return this->totalStepsMD;
+}
+
+void Parameters::SetTotalStepsMD(int totalSteps){
+   this->totalStepsMD = totalSteps;
+}
+
+double Parameters::GetTimeWidthMD(){
+   return this->timeWidthMD;
+}
+
+void Parameters::SetTimeWidthMD(double timeWidth){
+   this->timeWidthMD = timeWidth;
+}
+
 }
 #endif
 

--- a/src/input.in
+++ b/src/input.in
@@ -1,8 +1,8 @@
 // example of the input file
 THEORY
    //cndo/2
-   //indo
-   zindo/s
+   indo
+   //zindo/s
    //none 
    //principal_axes
    //translate
@@ -19,18 +19,21 @@ SCF
    diis_end_error 0.00000002
 SCF_END
 
-CIS
-   davidson yes
-   active_occ 100
-   active_vir 100
-   nstates 11
-   max_iter 200
-   max_dim 100
-   norm_tol 0.000001
-CIS_END
-
-
-
+//CIS
+//   davidson yes
+//   active_occ 100
+//   active_vir 100
+//   nstates 11
+//   max_iter 200
+//   max_dim 100
+//   norm_tol 0.000001
+//CIS_END
+
+MD
+//   total_steps 20
+//   electronic_state 2
+//   dt 0.2
+MD_END
 
 //INERTIA
 //   origin 1.0 2.0 30.0
@@ -50,7 +53,6 @@ CIS_END
    //difference 100.0 200.0 300.0
 //TRANSLATE_END
 
-
 // NH3
 //GEOMETRY
 //   N  0.950135    0.471698    0.000000
@@ -92,7 +94,6 @@ CIS_END
 //   H  -0.422611    0.820144    0.000000
 //GEOMETRY_END
 
-
 // c2
 //GEOMETRY
 //   C  0.168464    0.0    0.000000 
@@ -188,8 +189,6 @@ GEOMETRY_END
 //   Li  1.994960      0.485175      0.000000
 //GEOMETRY_END
 
-
-
 // Li2
 //GEOMETRY
 //   Li  0.0   0.0   1.230000
@@ -201,7 +200,6 @@ GEOMETRY_END
 //   Li  -1.570081   0.094340   0.0
 //   Li  -4.030081   0.094340   0.0
 //GEOMETRY_END
-//
 
 //GEOMETRY
 //  C         -3.402965    0.646900    0.000000

--- a/src/zindo/ZindoS.h
+++ b/src/zindo/ZindoS.h
@@ -22,7 +22,7 @@ public:
    ZindoS();
    ~ZindoS();
    void DoesCIS();
-   virtual void CalcForce(int electronicEigenIndex);
+   virtual void CalcForce(int electronicStateIndex);
 protected:
    virtual void CalcGammaAB(double** gammaAB, Molecule* molecule);
    virtual void SetMessages();
@@ -1424,9 +1424,9 @@ void ZindoS::CalcCISMatrix(double** matrixCIS, int numberOcc, int numberVir){
    cout << this->messageDoneCalcCISMatrix;
 }
 
-// eigenIndex is index of the electroinc eigen state.
-// "eigenIndex = 0" means electronic ground state. 
-void ZindoS::CalcForce(int electronicEigenIndex){
+// electronicStateIndex is index of the electroinc eigen state.
+// "electronicStateIndex = 0" means electronic ground state. 
+void ZindoS::CalcForce(int electronicStateIndex){
 
    // malloc or initialize Force matrix
    if(this->matrixForce == NULL){