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fix_srd.h
646d5bb1b9aaefficient_neuronet

fix_srd.h
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			/* -- c++ -- ----------------------------------------------------------
			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.
			------------------------------------------------------------------------- */

			#ifdef FIX_CLASS

			FixStyle(srd,FixSRD)

			#else

			#ifndef LMP_FIX_SRD_H
			#define LMP_FIX_SRD_H

			#include "fix.h"

			namespace LAMMPS_NS {

			class FixSRD : public Fix {
			public:
			FixSRD(class LAMMPS , int, char *);
			~FixSRD();
			int setmask();
			void init();
			void setup(int);
			void pre_neighbor();
			void post_force(int);
			double compute_vector(int);

			double memory_usage();
			int pack_reverse_comm(int, int, double *);
			void unpack_reverse_comm(int, int , double );

			private:
			int me,nprocs;
			int bigexist,biggroup,biggroupbit;
			int collidestyle,lamdaflag,overlap,insideflag,exactflag,maxbounceallow;
			int cubicflag,shiftuser,shiftseed,shiftflag,tstat;
			int rescale_rotate,rescale_collide;
			double gridsrd,gridsearch,lamda,radfactor,cubictol;
			int triclinic,change_size,change_shape,deformflag;

			double dt_big,dt_srd;
			double mass_big,mass_srd;
			double temperature_srd;
			double sigma;
			double srd_per_cell;
			double dmax,vmax,vmaxsq;
			double maxbigdiam,minbigdiam;
			double dist_ghost,dist_srd,dist_srd_reneigh; // explained in code

			int wallexist,nwall,wallvarflag;
			class FixWallSRD *wallfix;
			int *wallwhich;
			double xwall,xwallhold,*vwall;
			double **fwall;
			double walltrigger;

			class AtomVecEllipsoid *avec_ellipsoid;
			class AtomVecLine *avec_line;
			class AtomVecTri *avec_tri;

			// for orthogonal box, these are in box units
			// for triclinic box, these are in lamda units

			double srdlo[3],srdhi[3]; // SRDs must stay inside
			double srdlo_reneigh[3],srdhi_reneigh[3]; // SRDs trigger a reneigh

			int dimension;
			int initflag,setupflag,reneighflag;
			class RanMars *random;
			class RanPark *randomshift;

			// stats

			int ncheck,ncollide,ninside,nrescale,reneighcount;
			int nbounce,bouncemaxnum,bouncemax;
			int stats_flag;
			int srd_bin_count;
			double srd_bin_temp;
			double stats[12],stats_all[12];

			double **flocal; // local ptrs to atom force and torque
			double **tlocal;

			// info to store for each owned and ghost big particle and wall

			struct Big {
			int index; // local index of particle/wall
			int type; // SPHERE or ELLIPSOID or LINE or TRI or WALL
			double radius,radsq; // radius of sphere
			double aradsqinv; // 3 ellipsoid radii
			double bradsqinv;
			double cradsqinv;
			double length; // length of line segment
			double normbody[3]; // normal of tri in body-frame
			double cutbinsq; // add big to bin if within this distance
			double omega[3]; // current omega for sphere/ellipsoid/tri/line
			double ex[3],ey[3],ez[3]; // current orientation vecs for ellipsoid/tri
			double norm[3]; // current unit normal of tri in space-frame
			double theta; // current orientation of line
			};

			Big *biglist; // list of info for each owned & ghost big and wall
			int torqueflag; // 1 if any big particle is torqued

			// current size of particle-based arrays

			int nbig; // # of owned/ghost big particles and walls
			int maxbig; // max number of owned/ghost big particles and walls
			int nmax; // max number of SRD particles

			// bins for SRD velocity remap, shifting and communication
			// binsize and inv are in lamda units for triclinic

			int nbins1,nbin1x,nbin1y,nbin1z;
			double binsize1x,binsize1y,binsize1z;
			double bininv1x,bininv1y,bininv1z;

			struct BinAve {
			int owner; // 1 if I am owner of this bin, 0 if not
			int n; // # of SRD particles in bin
			double xctr[3]; // center point of bin, only used for triclinic
			double vsum[3]; // sum of v components for SRD particles in bin
			double random; // random value if I am owner
			double value[12]; // extra per-bin values
			};

			struct BinComm {
			int nsend,nrecv; // # of bins to send/recv
			int sendproc,recvproc; // who to send/recv to/from
			int sendlist,recvlist; // list of bins to send/recv
			};

			struct BinShift {
			int commflag; // 1 if this shift requires any comm
			int nbins,nbinx,nbiny,nbinz; // extent of my bins
			int maxbinsq,maxvbin;
			int binlo[3],binhi[3]; // extent of my bins in global array
			double corner[3]; // lower,left corner to offset from
			// corner is in lamda units for triclinic
			BinAve *vbin; // my bins
			BinComm bcomm[6]; // bin communication pattern for overlaps
			};
			BinShift shifts[2]; // 0 = no shift, 1 = shift

			int maxbin1;
			int *binhead; // 1st SRD particle in each bin
			int *binnext; // next SRD particle in same bin
			int maxbuf;
			double sbuf1,sbuf2; // buffers for send/recv of velocity bin data
			double rbuf1,rbuf2;

			// bins and stencil for collision searching for SRDs & big particles

			int nbins2,nbin2x,nbin2y,nbin2z;
			int maxbin2;
			double binsize2x,binsize2y,binsize2z;
			double bininv2x,bininv2y,bininv2z;
			double xblo2,yblo2,zblo2;

			int *nbinbig; // # of big particles overlapping each bin
			int **binbig; // indices of big particles overlapping each bin
			int *binsrd; // which bin each SRD particle is in
			int nstencil; // # of bins in stencil
			int maxstencil; // max # of bins stencil array can hold
			int **stencil; // list of 3d bin offsets a big particle can overlap

			// persistent data for line/tri collision calculations

			double tfraction,theta0,theta1;
			double xs0[3],xs1[3],xsc[3];
			double xb0[3],xb1[3],xbc[3];
			double nbc[3];

			// shared data for triangle collision calculations

			// private functions

			void reset_velocities();
			void vbin_comm(int);
			void vbin_pack(BinAve , int, int , double *);
			void vbin_unpack(double , BinAve , int, int *);

			void xbin_comm(int, int);
			void xbin_pack(BinAve , int, int , double *, int);
			void xbin_unpack(double , BinAve , int, int *, int);

			void collisions_single();
			void collisions_multi();

			int inside_sphere(double , double , Big *);
			int inside_ellipsoid(double , double , Big *);
			int inside_line(double , double , double , double , Big *, double);
			int inside_tri(double , double , double , double , Big *, double);
			int inside_wall(double *, int);

			double collision_sphere_exact(double , double , double , double ,
			Big , double , double , double );
			void collision_sphere_inexact(double , double ,
			Big , double , double , double );
			double collision_ellipsoid_exact(double , double , double , double ,
			Big , double , double , double );
			void collision_ellipsoid_inexact(double , double ,
			Big , double , double , double );
			double collision_line_exact(double , double , double , double ,
			Big , double, double , double , double );
			double collision_tri_exact(double , double , double , double ,
			Big , double, double , double , double );
			double collision_wall_exact(double , int, double ,
			double , double , double *);
			void collision_wall_inexact(double , int, double , double , double );

			void slip(double , double , double , Big ,
			double , double , double *);
			void slip_wall(double , int, double , double *);
			void noslip(double , double , double , Big , int,
			double , double , double *);

			void force_torque(double , double , double *,
			double , double , double *);
			void force_wall(double , double , int);

			int update_srd(int, double, double , double , double , double );

			void parameterize();
			void setup_bounds();
			void setup_velocity_bins();
			void setup_velocity_shift(int, int);
			void setup_search_bins();
			void setup_search_stencil();
			void big_static();
			void big_dynamic();

			double point_bin_distance(double *, int, int, int);
			double bin_bin_distance(int, int, int);
			void velocity_stats(int);

			double newton_raphson(double, double);
			void lineside(double, double &, double &);
			void triside(double, double &, double &);

			double distance(int, int);
			void print_collision(int, int, int, double, double,
			double , double , double *, int);
			};

			}

			#endif
			#endif

			/* ERROR/WARNING messages:

			E: Illegal ... command

			Self-explanatory. Check the input script syntax and compare to the
			documentation for the command. You can use -echo screen as a
			command-line option when running LAMMPS to see the offending line.

			E: Could not find fix srd group ID

			Self-explanatory.

			E: Fix srd requires newton pair on

			Self-explanatory.

			E: Fix srd requires ghost atoms store velocity

			Use the comm_modify vel yes command to enable this.

			E: Fix srd no-slip requires atom attribute torque

			This is because the SRD collisions will impart torque to the solute
			particles.

			E: Cannot change timestep once fix srd is setup

			This is because various SRD properties depend on the timestep
			size.

			E: Fix srd can only currently be used with comm_style brick

			This is a current restriction in LAMMPS.

			E: Cannot use fix wall/srd more than once

			Nor is their a need to since multiple walls can be specified
			in one command.

			W: Fix SRD walls overlap but fix srd overlap not set

			You likely want to set this in your input script.

			E: Using fix srd with inconsistent fix deform remap option

			When shearing the box in an SRD simulation, the remap v option for fix
			deform needs to be used.

			W: Using fix srd with box deformation but no SRD thermostat

			The deformation will heat the SRD particles so this can
			be dangerous.

			W: Fix srd SRD moves may trigger frequent reneighboring

			This is because the SRD particles may move long distances.

			E: Fix SRD: bad search bin assignment

			Something has gone wrong in your SRD model; try using more
			conservative settings.

			E: Fix SRD: bad stencil bin for big particle

			Something has gone wrong in your SRD model; try using more
			conservative settings.

			E: Fix SRD: too many big particles in bin

			Reset the ATOMPERBIN parameter at the top of fix_srd.cpp
			to a larger value, and re-compile the code.

			E: Fix SRD: too many walls in bin

			This should not happen unless your system has been setup incorrectly.

			E: Fix SRD: bad bin assignment for SRD advection

			Something has gone wrong in your SRD model; try using more
			conservative settings.

			E: SRD particle %d started inside big particle %d on step %ld bounce %d

			See the inside keyword if you want this message to be an error vs
			warning.

			W: SRD particle %d started inside big particle %d on step %ld bounce %d

			See the inside keyword if you want this message to be an error vs
			warning.

			E: SRD particle %d started inside wall %d on step %ld bounce %d

			See the inside keyword if you want this message to be an error vs
			warning.

			W: SRD particle %d started inside wall %d on step %ld bounce %d

			See the inside keyword if you want this message to be an error vs
			warning.

			E: Bad quadratic solve for particle/line collision

			This is an internal error. It should nornally not occur.

			E: Bad quadratic solve for particle/tri collision

			This is an internal error. It should nornally not occur.

			W: Fix srd particle moved outside valid domain

			This may indicate a problem with your simulation parameters.

			E: Big particle in fix srd cannot be point particle

			Big particles must be extended spheriods or ellipsoids.

			E: Cannot use lines with fix srd unless overlap is set

			This is because line segements are connected to each other.

			E: Cannot use tris with fix srd unless overlap is set

			This is because triangles are connected to each other.

			E: Fix srd requires SRD particles all have same mass

			Self-explanatory.

			E: Fewer SRD bins than processors in some dimension

			This is not allowed. Make your SRD bin size smaller.

			E: SRD bins for fix srd are not cubic enough

			The bin shape is not within tolerance of cubic. See the cubic
			keyword if you want this message to be an error vs warning.

			W: SRD bins for fix srd are not cubic enough

			The bin shape is not within tolerance of cubic. See the cubic
			keyword if you want this message to be an error vs warning.

			E: SRD bin size for fix srd differs from user request

			Fix SRD had to adjust the bin size to fit the simulation box. See the
			cubic keyword if you want this message to be an error vs warning.

			W: SRD bin size for fix srd differs from user request

			Fix SRD had to adjust the bin size to fit the simulation box. See the
			cubic keyword if you want this message to be an error vs warning.

			E: Fix srd lamda must be >= 0.6 of SRD grid size

			This is a requirement for accuracy reasons.

			W: SRD bin shifting turned on due to small lamda

			This is done to try to preserve accuracy.

			W: Fix srd grid size > 1/4 of big particle diameter

			This may cause accuracy problems.

			W: Fix srd viscosity < 0.0 due to low SRD density

			This may cause accuracy problems.

			W: Fix srd particles may move > big particle diameter

			This may cause accuracy problems.

			*/

lammps/src/SRD/fix_srd.h646d5bb1b9aaefficient_neuronet

fix_srd.hView Options

lammps/src/SRD/fix_srd.h
646d5bb1b9aaefficient_neuronet

fix_srd.h
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