cpp file for the compute command

The right file with the cpp code
2019-07-25 11:44:43 +02:00
parent 6e9252c847
commit 6710cc4052
1 changed files with 133 additions and 0 deletions
--- a/src/USER-MISC/compute_gyration_shape.cpp
+++ b/src/USER-MISC/compute_gyration_shape.cpp
@ -0,0 +1,133 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ *    Contributing author:  Evangelos Voyiatzis (Royal DSM)
+ * ------------------------------------------------------------------------- */
+
+
+#include <cmath>
+#include <cstring>
+#include "compute_gyration_shape.h"
+#include "math_extra.h"
+#include "update.h"
+#include "atom.h"
+#include "group.h"
+#include "domain.h"
+#include "error.h"
+#include "modify.h"
+#include "compute.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+ComputeGyrationShape::ComputeGyrationShape(LAMMPS *lmp, int narg, char **arg) :
+  Compute(lmp, narg, arg), id_gyration(NULL)
+{
+  if (narg != 4) error->all(FLERR,"Illegal compute gyration/shape command");
+
+  vector_flag = 1;
+  size_vector = 6;
+  extscalar = 0;
+  extvector = 0;
+
+  // ID of compute gyration 
+  int n = strlen(arg[3]) + 1;
+  id_gyration = new char[n];
+  strcpy(id_gyration,arg[3]);
+
+  init();
+
+  vector = new double[6];
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeGyrationShape::~ComputeGyrationShape()
+{
+  delete [] id_gyration;
+  delete [] vector;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeGyrationShape::init()
+{
+  // check that the compute gyration command exist
+  int icompute = modify->find_compute(id_gyration);
+  if (icompute < 0)
+    error->all(FLERR,"Compute gyration does not exist for compute gyration/shape");
+
+  // check the id_gyration corresponds really to a compute gyration command
+  c_gyration = (Compute *) modify->compute[icompute];
+  if (strcmp(c_gyration->style,"gyration") != 0)
+    error->all(FLERR,"Compute gyration/shape does not use gyration compute");
+}
+
+/* ----------------------------------------------------------------------
+   compute shape parameters based on the eigenvalues of the gyration tensor of group of atoms
+------------------------------------------------------------------------- */
+
+void ComputeGyrationShape::compute_vector()
+{
+  invoked_vector = update->ntimestep;
+
+  // get the gyration tensor from the compute gyration
+  int icompute = modify->find_compute(id_gyration);
+  Compute *compute = modify->compute[icompute];
+  compute->compute_vector();
+  double *gyration_tensor = compute->vector;
+
+  // call the function for the calculation of the eigenvalues
+  double ione[3][3], evalues[3], evectors[3][3];
+
+  ione[0][0] = gyration_tensor[0];
+  ione[1][1] = gyration_tensor[1];
+  ione[2][2] = gyration_tensor[2];
+  ione[0][1] = ione[1][0] = gyration_tensor[3];
+  ione[1][2] = ione[2][1] = gyration_tensor[4];
+  ione[0][2] = ione[2][0] = gyration_tensor[5];
+
+  int ierror = MathExtra::jacobi(ione,evalues,evectors);
+  if (ierror) error->all(FLERR, "Insufficient Jacobi rotations for gyration/shape");
+
+  // sort the eigenvalues according to their size with bubble sort
+  double t;
+  for (int i = 0; i < 3; i++) {
+    for (int j = 0; j < 2-i; j++) {
+      if (fabs(evalues[j]) < fabs(evalues[j+1])) {
+        t = evalues[j];
+        evalues[j] = evalues[j+1];
+        evalues[j+1] = t;
+      }
+    }
+  }
+
+  // compute the shape parameters of the gyration tensor
+  double sq_eigen_x = pow(evalues[0], 2);
+  double sq_eigen_y = pow(evalues[1], 2);
+  double sq_eigen_z = pow(evalues[2], 2);
+
+  double nominator = pow(sq_eigen_x, 2) + pow(sq_eigen_y, 2) + pow(sq_eigen_z, 2);
+  double denominator = pow(sq_eigen_x+sq_eigen_y+sq_eigen_z, 2);
+
+  vector[0] = evalues[0];
+  vector[1] = evalues[1];
+  vector[2] = evalues[2];
+  vector[3] = sq_eigen_z - 0.5*(sq_eigen_x + sq_eigen_y);
+  vector[4] = sq_eigen_y - sq_eigen_x;
+  vector[5] = 0.5*(3*nominator/denominator -1);
+
+}
+