提交: a4c877c5b378cf4244531dffe42910db615ca627 - MolDS (git)

Commit MetaInfo

• 修订版: a4c877c5b378cf4244531dffe42910db615ca627 (tree)
• 时间: 2011-01-06 20:30:44
• 作者: Mikiya Fujii <mikiya.fujii@gmai...>
• Commiter: Mikiya Fujii

Log Message

Logic for translating molecule is added.

git-svn-id: https://svn.sourceforge.jp/svnroot/molds/MolDS/trunk@41 1136aad2-a195-0410-b898-f5ea1d11b9d8

更改概述

• modified: doc/README.txt
• modified: src/MolDS.cpp
• modified: src/base/Enums.h
• modified: src/base/InputParser.h
• modified: src/base/Molecule.h
• modified: src/input.in

差异

--- a/doc/README.txt
+++ b/doc/README.txt
@@ -75,4 +75,23 @@ Rotate Molecule:
          ROTATE_END
 
 
+Translate Molecule:
+   Write "translate" in theory-directive.
+
+   E.g. 
+         THEORY
+            translate 
+         THEORY_END
+
+   -options
+    "difference" indicates difference for the translation in angstrom unit.
+    This option is written in translate-directive.
+    Default values are 0, 0, and 0.
+
+   E.g. 
+         TRANSLATE
+            difference 12 30 45
+         TRANSLATE_END
+
+
 

--- a/src/MolDS.cpp
+++ b/src/MolDS.cpp
@@ -120,6 +120,18 @@ int main(){
 
       }
 
+      // Translate molecule
+      else if(Parameters::GetInstance()->GetCurrentTheory() == Translate && runingNormally){
+         try{
+            molecule->Translate();
+         }
+         catch(MolDSException ex){
+            cout << ex.what() << endl;
+            runingNormally = false;
+         }
+
+      }
+
       // Rotate molecule
       else if(Parameters::GetInstance()->GetCurrentTheory() == Rotate && runingNormally){
          try{

--- a/src/base/Enums.h
+++ b/src/base/Enums.h
@@ -12,6 +12,7 @@ RENUMSTR_BEGIN( TheoryType, TheoryTypeStr )
    RENUMSTR( INDO,   "INDO" )
    RENUMSTR( ZINDOS, "ZINDO/S" )
    RENUMSTR( PrincipalAxes, "PrincipalAxes" )
+   RENUMSTR( Translate, "Translate" )
    RENUMSTR( Rotate, "Rotate" )
    RENUMSTR( NONE, "NONE" )
    RENUMSTR( TheoryType_end,  "TheoryType_end" )

--- a/src/base/InputParser.h
+++ b/src/base/InputParser.h
@@ -46,6 +46,7 @@ private:
    string stringTheoryINDO;
    string stringTheoryZINDOS;
    string stringTheoryPrincipalAxes;
+   string stringTheoryTranslate;
    string stringTheoryRotate;
    string stringTheoryNONE;
    string stringGeometry;
@@ -66,6 +67,9 @@ private:
    string stringRotatingType;
    string stringRotatingTypeAxis;
    string stringRotatingTypeEularAngle;
+   string stringTranslate;
+   string stringTranslateEnd;
+   string stringTranslatingDifference;
    void CalcMolecularBasics(Molecule* molecule);
    void OutputMolecularBasics(Molecule* molecule);
    void OutputScfConditions();
@@ -91,6 +95,7 @@ InputParser::InputParser(){
    this->stringTheoryINDO = "indo";
    this->stringTheoryZINDOS = "zindo/s";
    this->stringTheoryPrincipalAxes = "principal_axes";
+   this->stringTheoryTranslate = "translate";
    this->stringTheoryRotate = "rotate";
    this->stringTheoryNONE = "none";
    this->stringGeometry =    "geometry";
@@ -113,6 +118,9 @@ InputParser::InputParser(){
    this->stringRotatingType = "type";
    this->stringRotatingTypeAxis = "axis";
    this->stringRotatingTypeEularAngle = "eular_angle";
+   this->stringTranslate = "translate";
+   this->stringTranslateEnd = "translate_end";
+   this->stringTranslatingDifference = "difference";
 }
 
 InputParser::~InputParser(){
@@ -241,6 +249,23 @@ void InputParser::Parse(Molecule* molecule){
          i = j;
       }
       
+      // translating condition
+      if(inputTerms[i].compare(this->stringTranslate) == 0){
+         int j=i+1;
+         while(inputTerms[j].compare(this->stringTranslateEnd) != 0){
+            // origin
+            if(inputTerms[j].compare(this->stringTranslatingDifference) == 0){
+               double x = atof(inputTerms[j+1].c_str()) * Parameters::GetInstance()->GetAngstrom2AU();
+               double y = atof(inputTerms[j+2].c_str()) * Parameters::GetInstance()->GetAngstrom2AU();
+               double z = atof(inputTerms[j+3].c_str()) * Parameters::GetInstance()->GetAngstrom2AU();
+               molecule->SetTranslatingDifference(x, y, z);
+               j+=3;
+            }
+            j++;   
+         }
+         i = j;
+      }
+      
       // rotating condition
       if(inputTerms[i].compare(this->stringRotate) == 0){
          int j=i+1;
@@ -315,6 +340,11 @@ void InputParser::Parse(Molecule* molecule){
                Parameters::GetInstance()->SetCurrentTheory(PrincipalAxes);
             }
 
+            // Translate
+            else if(inputTerms[j].compare(this->stringTheoryTranslate) == 0){
+               Parameters::GetInstance()->SetCurrentTheory(Translate);
+            }
+
             // Rotate
             else if(inputTerms[j].compare(this->stringTheoryRotate) == 0){
                Parameters::GetInstance()->SetCurrentTheory(Rotate);

--- a/src/base/Molecule.h
+++ b/src/base/Molecule.h
@@ -35,6 +35,8 @@ public:
    void SetRotatingAngle(double angle);
    void SetRotatingEularAngles(double alpha, double beta, double gamma);
    void SetRotatingType(RotatingType rotatingType);
+   void SetTranslatingDifference(double x, double y, double z);
+   void Translate();
 private:
    vector<Atom*>* atomVect;
    double* COMXyz;
@@ -42,6 +44,7 @@ private:
    double* rotatingOrigin;
    double* rotatingAxis;
    double  rotatingAngle;
+   double* translatingDifference;
    EularAngle* rotatingEularAngles;
    RotatingType rotatingType;
    bool wasCalculatedCOMXyz;
@@ -52,6 +55,7 @@ private:
    void OutputPrincipalAxes(double** inertiaTensor, double* inertiaMoments);
    void OutputInertiaTensorOrigin();
    void OutputRotatingConditions();
+   void OutputTranslatingConditions();
    string messageTotalNumberAOs;
    string messageTotalNumberAtoms;
    string messageTotalNumberValenceElectrons;
@@ -81,6 +85,11 @@ private:
    string messageRotatingType;
    string messageRotatingEularAngles;
    string messageRotatingEularAnglesTitle;
+   string messageStartTranslate;
+   string messageDoneTranslate;
+   string messageTranslatingDifference;
+   string messageTranslatingDifferenceTitleAU;
+   string messageTranslatingDifferenceTitleAng;
 };
 
 Molecule::Molecule(){
@@ -102,8 +111,8 @@ Molecule::Molecule(){
    this->messageCOM = "\tCenter of Mass:\n";
    this->messageCOMTitleAU = "\t\t| x [a.u.] | y[a.u.] | z[a.u.] |\n";
    this->messageCOMTitleAng = "\t\t| x [angst.] | y[angst.] | z[angst.] |\n";
-   this->messageStartPrincipalAxes = "**********  START: Principal Axes Analysis  **********\n";
-   this->messageDonePrincipalAxes =  "**********  DONE: Principal Axes Analysis  ***********\n\n\n";
+   this->messageStartPrincipalAxes = "**********  START: Principal Axes of Inertia  **********\n";
+   this->messageDonePrincipalAxes =  "**********  DONE: Principal Axes of Inertia  ***********\n\n\n";
    this->messagePrincipalAxes = "\tPrincipal Axes:\n";
    this->messagePrincipalAxesTitleAU = "\t\t| inertia moments [a.u.] | x [a.u.] | y[a.u.] | z[a.u.] | (normalized)\n";
    this->messagePrincipalAxesTitleAng = "\t\t| inertia moments [g*angust**2/mol] | x [angst.] | y[angst.] | z[angst.] | (not normalized)\n";
@@ -122,6 +131,11 @@ Molecule::Molecule(){
    this->messageRotatingType = "\tType: ";
    this->messageRotatingEularAngles = "\tEular Angles:\n";
    this->messageRotatingEularAnglesTitle = "\t\t| alpha[degree] | beta[degree] | gamma[degree] |\n";
+   this->messageStartTranslate = "**********  START: Translate molecule  **********\n";
+   this->messageDoneTranslate =  "**********  DONE: Translate molecule  ***********\n\n\n";
+   this->messageTranslatingDifference = "\tTranslating Difference:\n";
+   this->messageTranslatingDifferenceTitleAU = "\t\t| x [a.u.] | y[a.u.] | z[a.u.] |\n";
+   this->messageTranslatingDifferenceTitleAng = "\t\t| x [angst.] | y[angst.] | z[angst.] |\n";
 }
 
 Molecule::~Molecule(){
@@ -159,6 +173,11 @@ Molecule::~Molecule(){
       this->rotatingEularAngles = NULL;
       //cout << "rotatingEularAngles deleted\n";
    }
+   if(this->translatingDifference != NULL){
+      MallocerFreer::GetInstance()->FreeDoubleMatrix1d(this->translatingDifference);
+      this->translatingDifference = NULL;
+      //cout << "translatingDifference deleted\n";
+   }
 }
 
 vector<Atom*>* Molecule::GetAtomVect(){
@@ -180,7 +199,7 @@ void Molecule::CalcCOMXyz(){
       double atomicMass;
 
       for(int j=0; j<3; j++){
-         this->COMXyz[j] += 0.0;
+         this->COMXyz[j] = 0.0;
       }
       
       for(int i=0; i<this->atomVect->size(); i++){
@@ -514,6 +533,62 @@ void Molecule::OutputRotatingConditions(){
                                     this->rotatingEularAngles->GetGamma()/degree2Radian);
    }
 
+}
+
+void Molecule::SetTranslatingDifference(double x, double y, double z){
+   if(this->translatingDifference == NULL){
+      this->translatingDifference = MallocerFreer::GetInstance()->MallocDoubleMatrix1d(3);
+   }
+
+   this->translatingDifference[0] = x;
+   this->translatingDifference[1] = y;
+   this->translatingDifference[2] = z;
+
+}
+
+void Molecule::Translate(){
+
+   cout << this->messageStartTranslate;
+
+   if(this->translatingDifference == NULL){
+      this->SetTranslatingDifference(0.0, 0.0, 0.0);
+   }
+
+
+   this->OutputTranslatingConditions(); 
+
+   Atom* atom;
+   for(int i=0; i<this->atomVect->size(); i++){
+         atom = (*this->atomVect)[i]; 
+         atom->GetXyz()[0] += this->translatingDifference[0];
+         atom->GetXyz()[1] += this->translatingDifference[1];
+         atom->GetXyz()[2] += this->translatingDifference[2];
+   }
+   
+   this->wasCalculatedCOMXyz = false;
+   this->CalcCOMXyz();
+
+   this->OutputConfiguration();
+   this->OutputCOMXyz();
+
+   cout << this->messageDoneTranslate;
+}
+
+void Molecule::OutputTranslatingConditions(){
+
+   double angst2AU = Parameters::GetInstance()->GetAngstrom2AU();
+
+   // rotating origin
+   cout << this->messageTranslatingDifference;
+   cout << this->messageTranslatingDifferenceTitleAng;
+   printf("\t\t%e\t%e\t%e\n\n",this->translatingDifference[0]/angst2AU,
+                               this->translatingDifference[1]/angst2AU,
+                               this->translatingDifference[2]/angst2AU);
+
+   cout << this->messageTranslatingDifferenceTitleAU;
+   printf("\t\t%e\t%e\t%e\n\n",this->translatingDifference[0],
+                               this->translatingDifference[1],
+                               this->translatingDifference[2]);
 
 }
 

--- a/src/input.in
+++ b/src/input.in
@@ -8,7 +8,8 @@ THEORY
    //indo
    //zindo/s
    //none 
-   principal_axes
+   //principal_axes
+   translate
    //rotate
 THEORY_END
 
@@ -17,14 +18,20 @@ INERTIA
 INERTIA_END
 
 ROTATE
-   type axis
+   //type axis
    //type eular_angle
-   origin 1.0 2.0 3.0
-   axis 3.0 4.0 5.0
-   angle 30
-   angles 15 25 35
+   //origin 1.0 2.0 3.0
+   //axis 3.0 4.0 5.0
+   //angle 30
+   //angles 15 25 35
 ROTATE_END
 
+TRANSLATE
+   //difference 100.0 200.0 300.0
+TRANSLATE_END
+
+
+
 //metane
 //GEOMETRY
 //   C  -0.37687006  0.95490165  0.00000000