forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5972 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
8cd382fef6
commit
2f7aaf73f4
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@ -5,7 +5,6 @@
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if (test $1 = 1) then
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cp atom_vec_ellipsoid.cpp ..
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cp compute_erotate_asphere.cpp ..
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cp compute_temp_asphere.cpp ..
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cp fix_nh_asphere.cpp ..
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@ -16,7 +15,6 @@ if (test $1 = 1) then
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cp pair_gayberne.cpp ..
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cp pair_resquared.cpp ..
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cp atom_vec_ellipsoid.h ..
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cp compute_erotate_asphere.h ..
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cp compute_temp_asphere.h ..
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cp fix_nh_asphere.h ..
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@ -33,7 +31,6 @@ if (test $1 = 1) then
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elif (test $1 = 0) then
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rm ../atom_vec_ellipsoid.cpp
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rm ../compute_erotate_asphere.cpp
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rm ../compute_temp_asphere.cpp
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rm ../fix_nh_asphere.cpp
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@ -44,7 +41,6 @@ elif (test $1 = 0) then
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rm ../pair_gayberne.cpp
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rm ../pair_resquared.cpp
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rm ../atom_vec_ellipsoid.h
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rm ../compute_erotate_asphere.h
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rm ../compute_temp_asphere.h
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rm ../fix_nh_asphere.h
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File diff suppressed because it is too large
Load Diff
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@ -1,91 +0,0 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifdef ATOM_CLASS
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AtomStyle(ellipsoid,AtomVecEllipsoid)
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#else
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#ifndef LMP_ATOM_VEC_ELLIPSOID_H
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#define LMP_ATOM_VEC_ELLIPSOID_H
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#include "atom_vec.h"
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namespace LAMMPS_NS {
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class AtomVecEllipsoid : public AtomVec {
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public:
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struct Bonus {
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double shape[3];
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double quat[4];
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int ilocal;
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};
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struct Bonus *bonus;
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AtomVecEllipsoid(class LAMMPS *, int, char **);
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~AtomVecEllipsoid();
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void grow(int);
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void grow_reset();
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void copy(int, int, int);
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int pack_comm(int, int *, double *, int, int *);
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int pack_comm_vel(int, int *, double *, int, int *);
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int pack_comm_hybrid(int, int *, double *);
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void unpack_comm(int, int, double *);
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void unpack_comm_vel(int, int, double *);
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int unpack_comm_hybrid(int, int, double *);
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int pack_reverse(int, int, double *);
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int pack_reverse_hybrid(int, int, double *);
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void unpack_reverse(int, int *, double *);
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int unpack_reverse_hybrid(int, int *, double *);
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int pack_border(int, int *, double *, int, int *);
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int pack_border_vel(int, int *, double *, int, int *);
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int pack_border_hybrid(int, int *, double *);
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void unpack_border(int, int, double *);
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void unpack_border_vel(int, int, double *);
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int unpack_border_hybrid(int, int, double *);
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int pack_exchange(int, double *);
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int unpack_exchange(double *);
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int size_restart();
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int pack_restart(int, double *);
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int unpack_restart(double *);
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void create_atom(int, double *);
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void data_atom(double *, int, char **);
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int data_atom_hybrid(int, char **);
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void data_vel(int, char **);
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int data_vel_hybrid(int, char **);
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bigint memory_usage();
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// manipulate Bonus data structure for extra atom info
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void grow_bonus();
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void copy_bonus(int, int);
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void set_bonus(int, double, double, double);
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void clear_bonus();
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void data_atom_bonus(int, char **);
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private:
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double PI;
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int *tag,*type,*mask,*image;
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double **x,**v,**f;
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double *rmass;
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double **angmom,**torque;
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int *ellipsoid;
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int nlocal_bonus,nghost_bonus,nmax_bonus;
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};
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}
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#endif
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#endif
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@ -16,6 +16,7 @@
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------------------------------------------------------------------------- */
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#include "mpi.h"
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#include "string.h"
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#include "compute_temp_asphere.h"
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#include "math_extra.h"
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#include "atom.h"
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@ -545,7 +545,8 @@ double PairGayBerne::gayberne_analytic(const int i,const int j,double a1[3][3],
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double g12[3][3];
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MathExtra::plus3(g1,g2,g12);
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double kappa[3];
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MathExtra::mldivide3(g12,r12,kappa,error);
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int ierror = MathExtra::mldivide3(g12,r12,kappa);
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if (error) error->all("Bad matrix inversion in mldivide3");
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// tempv = G12^-1*r12hat
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@ -575,7 +576,8 @@ double PairGayBerne::gayberne_analytic(const int i,const int j,double a1[3][3],
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double b12[3][3];
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double iota[3];
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MathExtra::plus3(b1,b2,b12);
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MathExtra::mldivide3(b12,r12,iota,error);
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ierror = MathExtra::mldivide3(b12,r12,iota);
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if (error) error->all("Bad matrix inversion in mldivide3");
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// tempv = G12^-1*r12hat
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@ -724,7 +726,8 @@ double PairGayBerne::gayberne_lj(const int i,const int j,double a1[3][3],
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g12[0][2] = g1[0][2]; g12[2][0] = g1[2][0];
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g12[1][2] = g1[1][2]; g12[2][1] = g1[2][1];
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double kappa[3];
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MathExtra::mldivide3(g12,r12,kappa,error);
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int ierror = MathExtra::mldivide3(g12,r12,kappa);
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if (error) error->all("Bad matrix inversion in mldivide3");
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// tempv = G12^-1*r12hat
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@ -759,7 +762,8 @@ double PairGayBerne::gayberne_lj(const int i,const int j,double a1[3][3],
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b12[0][1] = b1[0][1]; b12[1][0] = b1[1][0];
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b12[0][2] = b1[0][2]; b12[2][0] = b1[2][0];
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b12[1][2] = b1[1][2]; b12[2][1] = b1[2][1];
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MathExtra::mldivide3(b12,r12,iota,error);
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ierror = MathExtra::mldivide3(b12,r12,iota);
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if (error) error->all("Bad matrix inversion in mldivide3");
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// tempv = G12^-1*r12hat
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@ -612,7 +612,9 @@ double PairRESquared::resquared_analytic(const int i, const int j,
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double temp[3][3];
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MathExtra::plus3(wi.gamma,wj.gamma,temp);
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MathExtra::mldivide3(temp,rhat,s,error);
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int ierror = MathExtra::mldivide3(temp,rhat,s);
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if (error) error->all("Bad matrix inversion in mldivide3");
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sigma12 = 1.0/sqrt(0.5*MathExtra::dot3(s,rhat));
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MathExtra::times_column3(wi.A,rhat,z1);
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MathExtra::times_column3(wj.A,rhat,z2);
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@ -642,7 +644,9 @@ double PairRESquared::resquared_analytic(const int i, const int j,
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double temp2[3][3];
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MathExtra::times3(wj.aTe,wj.A,temp2);
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MathExtra::plus3(temp,temp2,temp);
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MathExtra::mldivide3(temp,rhat,w,error);
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ierror = MathExtra::mldivide3(temp,rhat,w);
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if (error) error->all("Bad matrix inversion in mldivide3");
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h12 = rnorm-sigma12;
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eta = lambda/nu;
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chi = 2.0*MathExtra::dot3(rhat,w);
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@ -894,14 +898,18 @@ double PairRESquared::resquared_lj(const int i, const int j,
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// energy
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MathExtra::mldivide3(gamma,rhat,s,error);
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int ierror = MathExtra::mldivide3(gamma,rhat,s);
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if (error) error->all("Bad matrix inversion in mldivide3");
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sigma12 = 1.0/sqrt(0.5*MathExtra::dot3(s,rhat));
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double temp[3][3];
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MathExtra::times3(wi.aTe,wi.A,temp);
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temp[0][0] += 1.0;
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temp[1][1] += 1.0;
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temp[2][2] += 1.0;
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MathExtra::mldivide3(temp,rhat,w,error);
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ierror = MathExtra::mldivide3(temp,rhat,w);
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if (error) error->all("Bad matrix inversion in mldivide3");
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h12 = rnorm-sigma12;
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chi = 2.0*MathExtra::dot3(rhat,w);
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sigh = sigma[type[i]][type[j]]/h12;
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