[ViewVC] Diff of: group/trunk/OOPSE/utils/MoLocator.cpp

Comparing trunk/OOPSE/utils/MoLocator.cpp (file contents):
Revision 501 by mmeineke, Tue Apr 15 21:20:35 2003 UTC vs.
Revision 538 by mmeineke, Sat May 17 16:57:08 2003 UTC

-+
+#include <iostream>
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+#include <cstdlib>
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+#include <cmath>
-+
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+#include "simError.h"
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+#include "MoLocator.hpp"
-+
-+
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+MoLocator::MoLocator( MoleculeStamp* theStamp ){
-+
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+  myStamp = theStamp;
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+  nAtoms = myStamp->getNAtoms();
-+
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+  myCoords = NULL;
-+
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+  calcRefCoords();
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+}
-+
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+MoLocator::~MoLocator(){
-+
-+
+  if( myCoords != NULL ) delete[] myCoords;
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+}
-+
-+
+void MoLocator::placeMol( double pos[3], double A[3][3], Atom** atomArray,
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+                          int atomIndex ){
-+
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+  int i,j,k;
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+  double r[3];
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+  double ux, uy, uz, u, uSqr;
-+
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+  AtomStamp* currAtom;
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+  DirectionalAtom* dAtom;
-+
-+
+  for(i=0; i<nAtoms; i++){
-+
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+    currAtom = myStamp->getAtom( i );
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+    j = atomIndex+i;
-+
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+    if( currAtom->haveOrientation()){
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+      dAtom = new DirectionalAtom( j );
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+      atomArray[j] = dAtom;
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+      ux = currAtom->getOrntX();
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+      uy = currAtom->getOrntY();
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+      uz = currAtom->getOrntZ();
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+      uSqr = (ux * ux) + (uy * uy) + (uz * uz);
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+      u = sqrt( uSqr );
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+      ux = ux / u;
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+      uy = uy / u;
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+      uz = uz / u;
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+      dAtom->setSUx( ux );
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+      dAtom->setSUy( uy );
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+      dAtom->setSUz( uz );
-+
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+      dAtom->setA( A );
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+      dAtom->setJx( 0.0 );
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+      dAtom->setJy( 0.0 );
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+      dAtom->setJz( 0.0 );
-+
-+
+    }
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+    else{
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+      atomArray[j] = new GeneralAtom( j );
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+    }
-+
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+    atomArray[j]->setType( currAtom->getType() );
-+
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+    for(k=0; k<3; k++) r[k] = myCoords[(i*3)+k];
-+
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+    rotMe( r, A );
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+    for(k=0; k<3; k++) r[k] += pos[k];
-+
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+    atomArray[j]->setX( r[0] );
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+    atomArray[j]->setY( r[1] );
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+    atomArray[j]->setZ( r[2] );
-+
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+    atomArray[j]->set_vx( 0.0 );
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+    atomArray[j]->set_vy( 0.0 );
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+    atomArray[j]->set_vz( 0.0 );
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+  }
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+}
-+
-+
+void MoLocator::calcRefCoords( void ){
-+
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+  int i,j,k;
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+  AtomStamp* currAtom;
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+  double centerX, centerY, centerZ;
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+  double smallX, smallY, smallZ;
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+  double bigX, bigY, bigZ;
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+  double dx, dy, dz;
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+  double dsqr;
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-+
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+  centerX = 0.0;
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+  centerY = 0.0;
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+  centerZ = 0.0;
-+
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+  for(i=0; i<nAtoms; i++){
-+
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+    currAtom = myStamp->getAtom(i);
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+    if( !currAtom->havePosition() ){
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+      sprintf( painCave.errMsg,
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+               "MoLocator error.\n"
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+               "  Component %s, atom %s does not have a position specified.\n"
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+               "  This means MoLocator cannot initalize it's position.\n",
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+               myStamp->getID(),
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+               currAtom->getType() );
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+      painCave.isFatal = 1;
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+      simError();
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+    }
-+
-+
-+
+    centerX += currAtom->getPosX();
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+    centerY += currAtom->getPosY();
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+    centerZ += currAtom->getPosZ();
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+  }
-+
-+
+  centerX /= nAtoms;
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+  centerY /= nAtoms;
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+  centerZ /= nAtoms;
-+
-+
+  myCoords = new double[nAtoms*3];
-+
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+  j = 0;
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+  for(i=0; i<nAtoms; i++){
-+
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+    currAtom = myStamp->getAtom(i);
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+    j = i*3;
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+    myCoords[j]   = currAtom->getPosX() - centerX;
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+    myCoords[j+1] = currAtom->getPosY() - centerY;
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+    myCoords[j+2] = currAtom->getPosZ() - centerZ;
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+  }
-+
-+
+  smallX = myCoords[0];
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+  smallY = myCoords[1];
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+  smallZ = myCoords[2];
-+
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+  bigX = myCoords[0];
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+  bigY = myCoords[1];
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+  bigZ = myCoords[2];
-+
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+  j=0;
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+  for(i=1; i<nAtoms; i++){
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+    j= i*3;
-+
-+
+    if( myCoords[j]   < smallX ) smallX = myCoords[j];
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+    if( myCoords[j+1] < smallY ) smallY = myCoords[j+1];
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+    if( myCoords[j+2] < smallZ ) smallZ = myCoords[j+2];
-+
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+    if( myCoords[j]   > bigX ) bigX = myCoords[j];
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+    if( myCoords[j+1] > bigY ) bigY = myCoords[j+1];
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+    if( myCoords[j+2] > bigZ ) bigZ = myCoords[j+2];
-+
+  }
-+
-+
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+  dx = bigX - smallX;
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+  dy = bigY - smallY;
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+  dz = bigZ - smallZ;
-+
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+  dsqr = (dx * dx) + (dy * dy) + (dz * dz);
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+  maxLength = sqrt( dsqr );
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+}
-+
-+
+void MoLocator::rotMe( double r[3], double A[3][3] ){
-+
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+  double rt[3];
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+  int i,j;
-+
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+  for(i=0; i<3; i++) rt[i] = r[i];
-+
-+
+  for(i=0; i<3; i++){
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+    r[i] = 0.0;
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+    for(j=0; j<3; j++){
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+      r[i] += A[i][j] * rt[j];
-+
+    }
-+
+  }
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+}

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Comparing trunk/OOPSE/utils/MoLocator.cpp (file contents): Revision 501 by mmeineke, Tue Apr 15 21:20:35 2003 UTC vs. Revision 538 by mmeineke, Sat May 17 16:57:08 2003 UTC

Diff Legend

Comparing trunk/OOPSE/utils/MoLocator.cpp (file contents):
Revision 501 by mmeineke, Tue Apr 15 21:20:35 2003 UTC vs.
Revision 538 by mmeineke, Sat May 17 16:57:08 2003 UTC