git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1414 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/MOLECULE/Install.csh

@@ -10,6 +10,7 @@ if ($1 == 1) then
   cp angle.cpp ..
   cp angle_charmm.cpp ..
   cp angle_cosine.cpp ..
+  cp angle_cosine_delta.cpp ..
   cp angle_cosine_squared.cpp ..
   cp angle_harmonic.cpp ..
   cp angle_hybrid.cpp ..
@@ -43,6 +44,7 @@ if ($1 == 1) then
 #  cp angle.h ..
   cp angle_charmm.h ..
   cp angle_cosine.h ..
+  cp angle_cosine_delta.h ..
   cp angle_cosine_squared.h ..
   cp angle_harmonic.h ..
   cp angle_hybrid.h ..
@@ -81,6 +83,7 @@ else if ($1 == 0) then
   rm ../angle.cpp
   rm ../angle_charmm.cpp
   rm ../angle_cosine.cpp
+  rm ../angle_cosine_delta.cpp
   rm ../angle_cosine_squared.cpp
   rm ../angle_harmonic.cpp
   rm ../angle_hybrid.cpp
@@ -114,6 +117,7 @@ else if ($1 == 0) then
 #  rm ../angle.h
   rm ../angle_charmm.h
   rm ../angle_cosine.h
+  rm ../angle_cosine_delta.h
   rm ../angle_cosine_squared.h
   rm ../angle_harmonic.h
   rm ../angle_hybrid.h

src/MOLECULE/angle_cosine_delta.cpp

@@ -0,0 +1,179 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   This software is distributed under the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Axel Kohlmeyer (U Penn), akohlmey at cmm.chem.upenn.edu
+------------------------------------------------------------------------- */
+
+#include "math.h"
+#include "stdlib.h"
+#include "angle_cosine_delta.h"
+#include "atom.h"
+#include "neighbor.h"
+#include "domain.h"
+#include "comm.h"
+#include "force.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define SMALL 0.001
+
+/* ---------------------------------------------------------------------- */
+
+AngleCosineDelta::AngleCosineDelta(LAMMPS *lmp) : AngleCosineSquared(lmp) {}
+
+/* ---------------------------------------------------------------------- */
+
+void AngleCosineDelta::compute(int eflag, int vflag)
+{
+  int i1,i2,i3,n,type;
+  double delx1,dely1,delz1,delx2,dely2,delz2,theta,dtheta,dcostheta,tk;
+  double eangle,f1[3],f3[3];
+  double rsq1,rsq2,r1,r2,c,a,cot,a11,a12,a22,b11,b12,b22,c0,s0,s;
+
+  eangle = 0.0;
+  if (eflag || vflag) ev_setup(eflag,vflag);
+  else evflag = 0;
+
+  double **x = atom->x;
+  double **f = atom->f;
+  int **anglelist = neighbor->anglelist;
+  int nanglelist = neighbor->nanglelist;
+  int nlocal = atom->nlocal;
+  int newton_bond = force->newton_bond;
+
+  for (n = 0; n < nanglelist; n++) {
+    i1 = anglelist[n][0];
+    i2 = anglelist[n][1];
+    i3 = anglelist[n][2];
+    type = anglelist[n][3];
+
+    // 1st bond
+
+    delx1 = x[i1][0] - x[i2][0];
+    dely1 = x[i1][1] - x[i2][1];
+    delz1 = x[i1][2] - x[i2][2];
+    domain->minimum_image(delx1,dely1,delz1);
+
+    rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
+    r1 = sqrt(rsq1);
+
+    // 2nd bond
+
+    delx2 = x[i3][0] - x[i2][0];
+    dely2 = x[i3][1] - x[i2][1];
+    delz2 = x[i3][2] - x[i2][2];
+    domain->minimum_image(delx2,dely2,delz2);
+
+    rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
+    r2 = sqrt(rsq2);
+
+    // angle (cos and sin)
+
+    c = delx1*delx2 + dely1*dely2 + delz1*delz2;
+    c /= r1*r2;
+      
+    if (c > 1.0) c = 1.0;
+    if (c < -1.0) c = -1.0;
+        
+    theta = acos(c);
+ 
+    s = sqrt(1.0 - c*c);
+    if (s < SMALL) s = SMALL;
+    s = 1.0/s;
+   
+    cot = c/s;
+ 
+    // force & energy
+	
+    dtheta = theta - theta0[type]; 
+    dcostheta = cos(dtheta);
+    tk = k[type] * (1.0-dcostheta);
+
+    if (eflag) eangle = tk;
+
+    a = -k[type];
+
+    // expand dtheta for cos and sin contribution to force
+    
+    a11 = a*c / rsq1;
+    a12 = -a / (r1*r2);
+    a22 = a*c / rsq2;
+    
+    b11 = -a*c*cot / rsq1;
+    b12 = a*cot / (r1*r2);
+    b22 = -a*c*cot / rsq2;
+        
+    c0 = cos(theta0[type]);
+    s0 = sin(theta0[type]);
+
+    f1[0] = (a11*delx1 + a12*delx2)*c0 + (b11*delx1 + b12*delx2)*s0;
+    f1[1] = (a11*dely1 + a12*dely2)*c0 + (b11*dely1 + b12*dely2)*s0;
+    f1[2] = (a11*delz1 + a12*delz2)*c0 + (b11*delz1 + b12*delz2)*s0;
+    f3[0] = (a22*delx2 + a12*delx1)*c0 + (b22*delx2 + b12*delx1)*s0;
+    f3[1] = (a22*dely2 + a12*dely1)*c0 + (b22*dely2 + b12*dely1)*s0;
+    f3[2] = (a22*delz2 + a12*delz1)*c0 + (b22*delz2 + b12*delz1)*s0;
+
+    // apply force to each of 3 atoms
+
+    if (newton_bond || i1 < nlocal) {
+      f[i1][0] += f1[0];
+      f[i1][1] += f1[1];
+      f[i1][2] += f1[2];
+    }
+
+    if (newton_bond || i2 < nlocal) {
+      f[i2][0] -= f1[0] + f3[0];
+      f[i2][1] -= f1[1] + f3[1];
+      f[i2][2] -= f1[2] + f3[2];
+    }
+
+    if (newton_bond || i3 < nlocal) {
+      f[i3][0] += f3[0];
+      f[i3][1] += f3[1];
+      f[i3][2] += f3[2];
+    }
+
+    if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
+			 delx1,dely1,delz1,delx2,dely2,delz2);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+double AngleCosineDelta::single(int type, int i1, int i2, int i3)
+{
+  double **x = atom->x;
+
+  double delx1 = x[i1][0] - x[i2][0];
+  double dely1 = x[i1][1] - x[i2][1];
+  double delz1 = x[i1][2] - x[i2][2];
+  domain->minimum_image(delx1,dely1,delz1);
+  double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
+  
+  double delx2 = x[i3][0] - x[i2][0];
+  double dely2 = x[i3][1] - x[i2][1];
+  double delz2 = x[i3][2] - x[i2][2];
+  domain->minimum_image(delx2,dely2,delz2);
+  double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
+
+  double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
+  c /= r1*r2;
+  if (c > 1.0) c = 1.0;
+  if (c < -1.0) c = -1.0;
+
+  double theta = acos(c);
+  double dtheta = theta - theta0[type];
+  double dcostheta = cos(dtheta);
+  double tk = k[type] * (1.0-dcostheta);
+  return tk;
+}

src/MOLECULE/angle_cosine_delta.h

@@ -0,0 +1,28 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   This software is distributed under the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifndef ANGLE_COSINE_DELTA_H
+#define ANGLE_COSINE_DELTA_H
+
+#include "stdio.h"
+#include "angle_cosine_squared.h"
+
+namespace LAMMPS_NS {
+
+class AngleCosineDelta : public AngleCosineSquared {
+ public:
+  AngleCosineDelta(class LAMMPS *);
+  void compute(int, int);
+  double single(int, int, int, int);
+};
+
+}
+
+#endif

src/MOLECULE/angle_cosine_squared.h

@@ -22,15 +22,15 @@ namespace LAMMPS_NS {
 class AngleCosineSquared : public Angle {
  public:
   AngleCosineSquared(class LAMMPS *);
-  ~AngleCosineSquared();
-  void compute(int, int);
+  virtual ~AngleCosineSquared();
+  virtual void compute(int, int);
   void coeff(int, int, char **);
   double equilibrium_angle(int);
   void write_restart(FILE *);
   void read_restart(FILE *);
-  double single(int, int, int, int);
+  virtual double single(int, int, int, int);
 
- private:
+ protected:
   double *k,*theta0;
 
   void allocate();

src/MOLECULE/style_molecule.h

@@ -14,6 +14,7 @@
 #ifdef AngleInclude
 #include "angle_charmm.h"
 #include "angle_cosine.h"
+#include "angle_cosine_delta.h"
 #include "angle_cosine_squared.h"
 #include "angle_harmonic.h"
 #include "angle_hybrid.h"
@@ -22,6 +23,7 @@
 #ifdef AngleClass
 AngleStyle(charmm,AngleCharmm)
 AngleStyle(cosine,AngleCosine)
+AngleStyle(cosine/delta,AngleCosineDelta)
 AngleStyle(cosine/squared,AngleCosineSquared)
 AngleStyle(harmonic,AngleHarmonic)
 AngleStyle(hybrid,AngleHybrid)