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cleanup of compute gyration/shape code.

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- use MathSpecial::square(x) instead of pow(x,2) for improved precision
and handling of small and negative numbers
- remove unused include statements
- no need to refetch the compute in every step. during init() is sufficient
This commit is contained in:
Axel Kohlmeyer
2019-07-29 16:16:24 -04:00
parent 0beb39c1af
commit 0820ebc143
2 changed files with 29 additions and 25 deletions
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47
src/USER-MISC/compute_gyration_shape.cpp
View File

@ -16,17 +16,14 @@
* ------------------------------------------------------------------------- */ * ------------------------------------------------------------------------- */
#include "compute_gyration_shape.h"
#include <cmath> #include <cmath>
#include <cstring> #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 "error.h"
#include "math_extra.h"
#include "math_special.h"
#include "modify.h" #include "modify.h"
#include "compute.h" #include "update.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -67,27 +64,26 @@ void ComputeGyrationShape::init()
// check that the compute gyration command exist // check that the compute gyration command exist
int icompute = modify->find_compute(id_gyration); int icompute = modify->find_compute(id_gyration);
if (icompute < 0) if (icompute < 0)
error->all(FLERR,"Compute gyration does not exist for compute gyration/shape"); error->all(FLERR,"Compute gyration ID does not exist for "
"compute gyration/shape");
// check the id_gyration corresponds really to a compute gyration command // check the id_gyration corresponds really to a compute gyration command
c_gyration = (Compute *) modify->compute[icompute]; c_gyration = (Compute *) modify->compute[icompute];
if (strcmp(c_gyration->style,"gyration") != 0) if (strcmp(c_gyration->style,"gyration") != 0)
error->all(FLERR,"Compute gyration/shape does not use gyration compute"); error->all(FLERR,"Compute gyration compute ID does not point to "
"gyration compute for compute gyration/shape");
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
compute shape parameters based on the eigenvalues of the gyration tensor of group of atoms compute shape parameters based on the eigenvalues of the
gyration tensor of group of atoms
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
void ComputeGyrationShape::compute_vector() void ComputeGyrationShape::compute_vector()
{ {
invoked_vector = update->ntimestep; invoked_vector = update->ntimestep;
c_gyration->compute_vector();
// get the gyration tensor from the compute gyration double *gyration_tensor = c_gyration->vector;
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 // call the function for the calculation of the eigenvalues
double ione[3][3], evalues[3], evectors[3][3]; double ione[3][3], evalues[3], evectors[3][3];
@ -100,7 +96,8 @@ void ComputeGyrationShape::compute_vector()
ione[0][2] = ione[2][0] = gyration_tensor[5]; ione[0][2] = ione[2][0] = gyration_tensor[5];
int ierror = MathExtra::jacobi(ione,evalues,evectors); int ierror = MathExtra::jacobi(ione,evalues,evectors);
if (ierror) error->all(FLERR, "Insufficient Jacobi rotations for gyration/shape"); if (ierror) error->all(FLERR, "Insufficient Jacobi rotations "
"for gyration/shape");
// sort the eigenvalues according to their size with bubble sort // sort the eigenvalues according to their size with bubble sort
double t; double t;
@ -115,19 +112,19 @@ void ComputeGyrationShape::compute_vector()
} }
// compute the shape parameters of the gyration tensor // compute the shape parameters of the gyration tensor
double sq_eigen_x = pow(evalues[0], 2); double sq_eigen_x = MathSpecial::square(evalues[0]);
double sq_eigen_y = pow(evalues[1], 2); double sq_eigen_y = MathSpecial::square(evalues[1]);
double sq_eigen_z = pow(evalues[2], 2); double sq_eigen_z = MathSpecial::square(evalues[2]);
double nominator = pow(sq_eigen_x, 2) + pow(sq_eigen_y, 2) + pow(sq_eigen_z, 2); double nominator = MathSpecial::square(sq_eigen_x)
double denominator = pow(sq_eigen_x+sq_eigen_y+sq_eigen_z, 2); + MathSpecial::square(sq_eigen_y)
+ MathSpecial::square(sq_eigen_z);
double denominator = MathSpecial::square(sq_eigen_x+sq_eigen_y+sq_eigen_z);
vector[0] = evalues[0]; vector[0] = evalues[0];
vector[1] = evalues[1]; vector[1] = evalues[1];
vector[2] = evalues[2]; vector[2] = evalues[2];
vector[3] = sq_eigen_z - 0.5*(sq_eigen_x + sq_eigen_y); vector[3] = sq_eigen_z - 0.5*(sq_eigen_x + sq_eigen_y);
vector[4] = sq_eigen_y - sq_eigen_x; vector[4] = sq_eigen_y - sq_eigen_x;
vector[5] = 0.5*(3*nominator/denominator -1); vector[5] = 0.5*(3*nominator/denominator - 1.0);
} }

7
src/USER-MISC/compute_gyration_shape.h
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@ -50,4 +50,11 @@ Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line. command-line option when running LAMMPS to see the offending line.
E: Compute gyration ID does not exist for compute gyration/shape
Self-explanatory. Provide a valid compute ID
E: Compute gyration/shape compute ID does not point to a gyration compute
Self-explanatory. Provide an ID of a compute gyration command.
*/ */