提交: 1531b73cc99dd7095858af1070dcd35ff898b75f - MolDS (git)

Commit MetaInfo

• 修订版: 1531b73cc99dd7095858af1070dcd35ff898b75f (tree)
• 时间: 2010-11-28 11:17:35
• 作者: Mikiya Fujii <mikiya.fujii@gmai...>
• Commiter: Mikiya Fujii

Log Message

refferences are added. Some modification for Sulfer is also added.

git-svn-id: https://svn.sourceforge.jp/svnroot/molds/MolDS/trunk@7 1136aad2-a195-0410-b898-f5ea1d11b9d8

更改概述

• add: doc/refferences.txt
• modified: src/MolDS.cpp
• modified: src/base/InputParser.h
• modified: src/cndo/Cndo2.h
• modified: src/input.in

差异

--- /dev/null
+++ b/doc/refferences.txt
@@ -0,0 +1,9 @@
+[PSS_1965] J. A. Pople, D. P. Santry, and G. A. Segal, J. Chem. Phys., 43, S129 (1965)
+[PS_1965] J. A. Pople and G. A. Segal, J. Chem. Phys., 43, S136 (1965)
+[PS_1966] J. A. Pople and G. A. Segal, J. Chem. Phys., 44, 3289 (1966)
+[PB_1970] J. A. Pople and D. L. Beveridge, "Approximate Molecular Orbital Theory", ISBN-13:978-0070505124 (1970)
+[BFB_1997] M. A. Blanco, M. Fl{\'o}rez, and M. Bermejo, J. Mol. Struct. 419, 19 (1997)
+
+
+
+

--- a/src/MolDS.cpp
+++ b/src/MolDS.cpp
@@ -15,6 +15,7 @@
 #include"base/atoms/Hatom.h"
 #include"base/atoms/Catom.h"
 #include"base/atoms/Liatom.h"
+#include"base/atoms/Satom.h"
 #include"base/MallocerFreer.h"
 #include"base/InputParser.h"
 #include"base/Utilities.h"
@@ -54,12 +55,10 @@ int main(){
    InputParser::GetInstance()->Parse(molecule);
 
    // cndo2
-   /*
    MolDS_cndo::Cndo2* cndo2 = new MolDS_cndo::Cndo2();
    cndo2->SetMolecule(molecule);
    cndo2->DoesSCF();
    delete cndo2;
-   */
 
    // indo
    MolDS_indo::Indo* indo = new MolDS_indo::Indo();
@@ -68,7 +67,6 @@ int main(){
    delete indo;
 
 
-
    /*** test lapack ***
    {
    int size = 3;

--- a/src/base/InputParser.h
+++ b/src/base/InputParser.h
@@ -165,6 +165,9 @@ void InputParser::Parse(Molecule* molecule){
             else if(inputTerms[j] == "c"){
                molecule->GetAtomVect()->push_back(new Catom(x, y, z));
             }
+            else if(inputTerms[j] == "s"){
+               molecule->GetAtomVect()->push_back(new Satom(x, y, z));
+            }
             j += 4;
          }
          i = j;

--- a/src/cndo/Cndo2.h
+++ b/src/cndo/Cndo2.h
@@ -659,7 +659,7 @@ void Cndo2::CalcOverlap(double** overlap, Molecule* molecule){
 
 }
 
-// see J. Mol. Struc. (Theochem), 419, 19 (1997)
+// see J. Mol. Struc. (Theochem), 419, 19 (1997) (ref. [BFB_1997])
 // we set gamma=0 always.
 void Cndo2::CalcRotatingMatrix(double** rotatingMatrix, Atom* atomA, Atom* atomB){
    MallocerFreer::GetInstance()->InitializeDoubleMatrix2d
@@ -677,7 +677,7 @@ void Cndo2::CalcRotatingMatrix(double** rotatingMatrix, Atom* atomA, Atom* atomB
    rotatingMatrix[s][s] = 1.0;
 
    // rotating matrix for p-function
-   // dMatrix is (53) with gamma=0 in J. Mol. Strct. 419, 19(1997) 
+   // dMatrix is (53) with gamma=0 in J. Mol. Strct. 419, 19(1997) (ref. [BFB_1997])
    rotatingMatrix[py][py] = cos(alpha);
    rotatingMatrix[py][pz] = sin(alpha)*sin(beta);
    rotatingMatrix[py][px] = sin(alpha)*cos(beta);
@@ -691,7 +691,7 @@ void Cndo2::CalcRotatingMatrix(double** rotatingMatrix, Atom* atomA, Atom* atomB
    rotatingMatrix[px][px] = cos(alpha)*cos(beta);
 
    // rotating matrix for d-function
-   // dMatrix is (37) in J. Mol. Strct. 419, 19(1997)
+   // dMatrix is (37) in J. Mol. Strct. 419, 19(1997) (ref. [BFB_1997])
    double** dMatrix;
    dMatrix =  MallocerFreer::GetInstance()->MallocDoubleMatrix2d
               (OrbitalType_end, OrbitalType_end);

--- a/src/input.in
+++ b/src/input.in
@@ -32,6 +32,13 @@ SCF_END
 //   C 0.0  1.369664    0.673854    
 //GEOMETRY_END
 
+// sh2
+GEOMETRY
+     S       -0.559299    0.471698    0.000000
+     H        0.750701    0.471698    0.000000
+     H       -0.996586    1.706558    0.000000
+GEOMETRY_END
+
 // benzene
 //GEOMETRY
 //   C  -0.505391      0.552561      0.000000
@@ -113,40 +120,40 @@ SCF_END
 //GEOMETRY_END
 //
 
-GEOMETRY
-  C         -3.402965    0.646900    0.000000
-  C         -2.007805    0.646900    0.000000
-  C         -1.310267    1.854651    0.000000
-  C         -2.007921    3.063160   -0.001199
-  C         -3.402746    3.063082   -0.001678
-  C         -4.100347    1.854876   -0.000682
-  H         -3.952724   -0.305417    0.000450
-  H         -1.458297   -0.305613    0.001315
-  H         -1.457721    4.015303   -0.001258
-  H         -3.952868    4.015363   -0.002631
-  H         -5.199951    1.855059   -0.000862
-  C          0.229733    1.854763    0.000888
-  C          0.927166    3.063092    0.000888
-  C          0.927326    0.646909    0.001803
-  C          2.321878    3.063471    0.001121
-  H          0.376905    4.015169   -0.000612
-  C          2.322463    0.647116    0.003033
-  H          0.377798   -0.305534    0.001984
-  C          3.019797    1.855115    0.002554
-  H          2.871672    4.015848    0.000487
-  H          2.872217   -0.305378    0.004170
-  C          4.559797    1.855884    0.002894
-  C          5.257921    0.647955    0.004326
-  C          5.256700    3.064136    0.001659
-  C          6.652633    0.648374    0.005205
-  H          4.708203   -0.304436    0.006077
-  C          6.651838    3.064727    0.001542
-  H          4.706627    4.016264    0.000350
-  C          7.349861    1.857127    0.003453
-  H          7.202970   -0.303688    0.006968
-  H          7.201047    4.017534    0.000153
-  H          8.449541    1.857208    0.004087
-GEOMETRY_END
+//GEOMETRY
+//  C         -3.402965    0.646900    0.000000
+//  C         -2.007805    0.646900    0.000000
+//  C         -1.310267    1.854651    0.000000
+//  C         -2.007921    3.063160   -0.001199
+//  C         -3.402746    3.063082   -0.001678
+//  C         -4.100347    1.854876   -0.000682
+//  H         -3.952724   -0.305417    0.000450
+//  H         -1.458297   -0.305613    0.001315
+//  H         -1.457721    4.015303   -0.001258
+//  H         -3.952868    4.015363   -0.002631
+//  H         -5.199951    1.855059   -0.000862
+//  C          0.229733    1.854763    0.000888
+//  C          0.927166    3.063092    0.000888
+//  C          0.927326    0.646909    0.001803
+//  C          2.321878    3.063471    0.001121
+//  H          0.376905    4.015169   -0.000612
+//  C          2.322463    0.647116    0.003033
+//  H          0.377798   -0.305534    0.001984
+//  C          3.019797    1.855115    0.002554
+//  H          2.871672    4.015848    0.000487
+//  H          2.872217   -0.305378    0.004170
+//  C          4.559797    1.855884    0.002894
+//  C          5.257921    0.647955    0.004326
+//  C          5.256700    3.064136    0.001659
+//  C          6.652633    0.648374    0.005205
+//  H          4.708203   -0.304436    0.006077
+//  C          6.651838    3.064727    0.001542
+//  H          4.706627    4.016264    0.000350
+//  C          7.349861    1.857127    0.003453
+//  H          7.202970   -0.303688    0.006968
+//  H          7.201047    4.017534    0.000153
+//  H          8.449541    1.857208    0.004087
+//GEOMETRY_END