git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9456 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -8,6 +8,7 @@ if (test $1 = 1) then
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cp fix_rigid_npt.cpp ..
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cp fix_rigid_nve.cpp ..
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cp fix_rigid_nvt.cpp ..
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cp fix_rigid_small.cpp ..
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cp fix_rigid.h ..
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cp fix_rigid_nh.h ..
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@ -15,6 +16,7 @@ if (test $1 = 1) then
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cp fix_rigid_npt.h ..
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cp fix_rigid_nve.h ..
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cp fix_rigid_nvt.h ..
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cp fix_rigid_small.h ..
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elif (test $1 = 0) then
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@ -24,6 +26,7 @@ elif (test $1 = 0) then
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rm -f ../fix_rigid_npt.cpp
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rm -f ../fix_rigid_nve.cpp
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rm -f ../fix_rigid_nvt.cpp
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rm -f ../fix_rigid_small.cpp
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rm -f ../fix_rigid.h
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rm -f ../fix_rigid_nh.h
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@ -31,6 +34,7 @@ elif (test $1 = 0) then
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rm -f ../fix_rigid_npt.h
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rm -f ../fix_rigid_nve.h
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rm -f ../fix_rigid_nvt.h
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rm -f ../fix_rigid_small.h
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fi
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2550
src/RIGID/fix_rigid_small.cpp
Normal file
2550
src/RIGID/fix_rigid_small.cpp
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File diff suppressed because it is too large
Load Diff
252
src/RIGID/fix_rigid_small.h
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252
src/RIGID/fix_rigid_small.h
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@ -0,0 +1,252 @@
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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 FIX_CLASS
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FixStyle(rigid/small,FixRigidSmall)
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#else
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#ifndef LMP_FIX_RIGID_SMALL_H
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#define LMP_FIX_RIGID_SMALL_H
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#include "fix.h"
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// replace this later
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#include <map>
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namespace LAMMPS_NS {
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class FixRigidSmall : public Fix {
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public:
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// static variable for ring communication callback to access
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static FixRigidSmall *frsptr;
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FixRigidSmall(class LAMMPS *, int, char **);
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virtual ~FixRigidSmall();
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virtual int setmask();
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virtual void init();
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virtual void setup(int);
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virtual void initial_integrate(int);
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void post_force(int);
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virtual void final_integrate();
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void initial_integrate_respa(int, int, int);
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void final_integrate_respa(int, int);
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double memory_usage();
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void grow_arrays(int);
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void copy_arrays(int, int, int);
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void set_arrays(int);
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int pack_exchange(int, double *);
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int unpack_exchange(int, double *);
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int pack_comm(int, int *, double *, int, int *);
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void unpack_comm(int, int, double *);
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int pack_reverse_comm(int, int, double *);
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void unpack_reverse_comm(int, int *, double *);
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void pre_neighbor();
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int dof(int);
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void deform(int);
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void reset_dt();
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protected:
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int me,nprocs;
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double dtv,dtf,dtq;
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double *step_respa;
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int triclinic;
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double MINUSPI,TWOPI;
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int firstflag; // 1 for first-time setup of rigid bodies
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int commflag; // various modes of forward/reverse comm
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int nbody; // total # of rigid bodies
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struct Body {
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double mass; // total mass of body
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double xcm[3]; // COM position
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double vcm[3]; // COM velocity
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double fcm[3]; // force on COM
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double torque[3]; // torque on COM
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double quat[4]; // quaternion for orientation of body
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double inertia[3]; // 3 principal components of inertia
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double itensor[6]; // 6 space-frame components of inertia tensor
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double ex_space[3]; // principal axes in space coords
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double ey_space[3];
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double ez_space[3];
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double angmom[3]; // angular momentum of body
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double omega[3]; // omega of body
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tagint image; // image flags of xcm
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int remapflag[4]; // PBC remap flags
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int ilocal; // index of owning atom
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};
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Body *body; // list of rigid bodies, owned and ghost
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int nlocal_body; // # of owned rigid bodies
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int nghost_body; // # of ghost rigid bodies
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int nmax_body; // max # of bodies that body can hold
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int bodysize; // sizeof(Body) in doubles
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// per-atom quantities
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// only defined for owned atoms, except bodyown for own+ghost
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int *bodyown; // index of body if atom owns a body, -1 if not
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int *bodytag; // ID of body this atom is in, 0 if none
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// ID = tag of atom that owns body
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int *atom2body; // index of owned/ghost body this atom is in, -1 if not
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// can point to original or any image of the body
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double **displace; // displacement of each atom in body coords
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int *eflags; // flags for extended particles
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double **orient; // orientation vector of particle wrt rigid body
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double **dorient; // orientation of dipole mu wrt rigid body
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int extended; // 1 if any particles have extended attributes
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int orientflag; // 1 if particles store spatial orientation
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int dorientflag; // 1 if particles store dipole orientation
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int POINT,SPHERE,ELLIPSOID,LINE,TRIANGLE,DIPOLE; // bitmasks for eflags
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int OMEGA,ANGMOM,TORQUE;
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class AtomVecEllipsoid *avec_ellipsoid;
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class AtomVecLine *avec_line;
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class AtomVecTri *avec_tri;
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int **counts;
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// Langevin thermostatting
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int langflag; // 0/1 = no/yes Langevin thermostat
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double t_start,t_stop,t_period; // thermostat params
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double **langextra; // Langevin thermostat forces and torques
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int maxlang; // max size of langextra
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class RanMars *random; // RNG
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// class data used by ring communication callbacks
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std::map<int,int> *hash;
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double **bbox;
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double **ctr;
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int *idclose;
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double *rsqclose;
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void set_xv();
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void set_v();
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void create_bodies();
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void setup_bodies();
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void grow_body();
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void reset_atom2body();
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// callback functions for ring communication
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static void bbox_update(int, char *);
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static void nearest_update(int, char *);
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// debug
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void check(int);
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};
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}
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#endif
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#endif
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/* ERROR/WARNING messages:
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E: Illegal ... command
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Self-explanatory. Check the input script syntax and compare to the
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documentation for the command. You can use -echo screen as a
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command-line option when running LAMMPS to see the offending line.
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E: Fix rigid molecule requires atom attribute molecule
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Self-explanatory.
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E: Could not find fix rigid group ID
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A group ID used in the fix rigid command does not exist.
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E: One or more atoms belong to multiple rigid bodies
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Two or more rigid bodies defined by the fix rigid command cannot
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contain the same atom.
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E: No rigid bodies defined
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The fix specification did not end up defining any rigid bodies.
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E: Fix rigid z force cannot be on for 2d simulation
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Self-explanatory.
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E: Fix rigid xy torque cannot be on for 2d simulation
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Self-explanatory.
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E: Fix rigid langevin period must be > 0.0
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Self-explanatory.
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E: One or zero atoms in rigid body
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Any rigid body defined by the fix rigid command must contain 2 or more
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atoms.
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W: More than one fix rigid
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It is not efficient to use fix rigid more than once.
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E: Rigid fix must come before NPT/NPH fix
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NPT/NPH fix must be defined in input script after all rigid fixes,
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else the rigid fix contribution to the pressure virial is
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incorrect.
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W: Computing temperature of portions of rigid bodies
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The group defined by the temperature compute does not encompass all
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the atoms in one or more rigid bodies, so the change in
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degrees-of-freedom for the atoms in those partial rigid bodies will
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not be accounted for.
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E: Fix rigid atom has non-zero image flag in a non-periodic dimension
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You cannot set image flags for non-periodic dimensions.
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E: Insufficient Jacobi rotations for rigid body
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Eigensolve for rigid body was not sufficiently accurate.
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E: Fix rigid: Bad principal moments
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The principal moments of inertia computed for a rigid body
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are not within the required tolerances.
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E: Cannot open fix rigid infile %s
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UNDOCUMENTED
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E: Unexpected end of fix rigid file
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UNDOCUMENTED
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E: Incorrect rigid body format in fix rigid file
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UNDOCUMENTED
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E: Invalid rigid body ID in fix rigid file
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UNDOCUMENTED
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*/
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