git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11979 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/comm_brick.h

@@ -0,0 +1,164 @@
+/* ----------------------------------------------------------------------
+   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.
+------------------------------------------------------------------------- */
+
+#ifndef LMP_COMM_BRICK_H
+#define LMP_COMM_BRICK_H
+
+#include "comm.h"
+
+namespace LAMMPS_NS {
+
+class CommBrick : public Comm {
+ public:
+  CommBrick(class LAMMPS *);
+  virtual ~CommBrick();
+
+  virtual void init();
+  virtual void setup();                        // setup 3d comm pattern
+  virtual void forward_comm(int dummy = 0);    // forward comm of atom coords
+  virtual void reverse_comm();                 // reverse comm of forces
+  virtual void exchange();                     // move atoms to new procs
+  virtual void borders();                      // setup list of atoms to comm
+
+  virtual void forward_comm_pair(class Pair *);    // forward comm from a Pair
+  virtual void reverse_comm_pair(class Pair *);    // reverse comm from a Pair
+  virtual void forward_comm_fix(class Fix *);      // forward comm from a Fix
+  virtual void reverse_comm_fix(class Fix *);      // reverse comm from a Fix
+  virtual void forward_comm_variable_fix(class Fix *); // variable-size variant
+  virtual void reverse_comm_variable_fix(class Fix *); // variable-size variant
+  virtual void forward_comm_compute(class Compute *);  // forward from a Compute
+  virtual void reverse_comm_compute(class Compute *);  // reverse from a Compute
+  virtual void forward_comm_dump(class Dump *);    // forward comm from a Dump
+  virtual void reverse_comm_dump(class Dump *);    // reverse comm from a Dump
+
+  void forward_comm_array(int, double **);         // forward comm of array
+  int exchange_variable(int, double *, double *&);  // exchange on neigh stencil
+  virtual bigint memory_usage();
+
+ protected:
+  int nswap;                        // # of swaps to perform = sum of maxneed
+  int recvneed[3][2];               // # of procs away I recv atoms from
+  int sendneed[3][2];               // # of procs away I send atoms to
+  int maxneed[3];                   // max procs away any proc needs, per dim
+  int triclinic;                    // 0 if domain is orthog, 1 if triclinic
+  int maxswap;                      // max # of swaps memory is allocated for
+  int size_forward;                 // # of per-atom datums in forward comm
+  int size_reverse;                 // # of datums in reverse comm
+  int size_border;                  // # of datums in forward border comm
+  int *sendnum,*recvnum;            // # of atoms to send/recv in each swap
+  int *sendproc,*recvproc;          // proc to send/recv to/from at each swap
+  int *size_forward_recv;           // # of values to recv in each forward comm
+  int *size_reverse_send;           // # to send in each reverse comm
+  int *size_reverse_recv;           // # to recv in each reverse comm
+  double *slablo,*slabhi;           // bounds of slab to send at each swap
+  double **multilo,**multihi;       // bounds of slabs for multi-type swap
+  double **cutghostmulti;           // cutghost on a per-type basis
+  int *pbc_flag;                    // general flag for sending atoms thru PBC
+  int **pbc;                        // dimension flags for PBC adjustments
+  int comm_x_only,comm_f_only;      // 1 if only exchange x,f in for/rev comm
+  int map_style;                    // non-0 if global->local mapping is done
+
+  int *firstrecv;                   // where to put 1st recv atom in each swap
+  int **sendlist;                   // list of atoms to send in each swap
+  int *maxsendlist;                 // max size of send list for each swap
+
+  double *buf_send;                 // send buffer for all comm
+  double *buf_recv;                 // recv buffer for all comm
+  int maxsend,maxrecv;              // current size of send/recv buffer
+  int maxforward,maxreverse;        // max # of datums in forward/reverse comm
+
+  int maxexchange;                  // max # of datums/atom in exchange comm 
+  int bufextra;                     // extra space beyond maxsend in send buffer
+
+  int updown(int, int, int, double, int, double *);
+                                            // compare cutoff to procs
+  virtual void grow_send(int, int);         // reallocate send buffer
+  virtual void grow_recv(int);              // free/allocate recv buffer
+  virtual void grow_list(int, int);         // reallocate one sendlist
+  virtual void grow_swap(int);              // grow swap and multi arrays
+  virtual void allocate_swap(int);          // allocate swap arrays
+  virtual void allocate_multi(int);         // allocate multi arrays
+  virtual void free_swap();                 // free swap arrays
+  virtual void free_multi();                // free multi arrays
+};
+
+}
+
+#endif
+
+/* ERROR/WARNING messages:
+
+W: OMP_NUM_THREADS environment is not set.
+
+This environment variable must be set appropriately to use the
+USER-OMP pacakge.
+
+E: Bad grid of processors
+
+The 3d grid of processors defined by the processors command does not
+match the number of processors LAMMPS is being run on.
+
+E: Processor count in z must be 1 for 2d simulation
+
+Self-explanatory.
+
+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: Invalid group in communicate command
+
+Self-explanatory.
+
+E: Communicate group != atom_modify first group
+
+Self-explanatory.
+
+E: Invalid cutoff in communicate command
+
+Specified cutoff must be >= 0.0.
+
+E: Specified processors != physical processors
+
+The 3d grid of processors defined by the processors command does not
+match the number of processors LAMMPS is being run on.
+
+E: Cannot use processors part command without using partitions
+
+See the command-line -partition switch.
+
+E: Invalid partitions in processors part command
+
+Valid partitions are numbered 1 to N and the sender and receiver
+cannot be the same partition.
+
+E: Sending partition in processors part command is already a sender
+
+Cannot specify a partition to be a sender twice.
+
+E: Receiving partition in processors part command is already a receiver
+
+Cannot specify a partition to be a receiver twice.
+
+E: Processors grid numa and map style are incompatible
+
+Using numa for gstyle in the processors command requires using
+cart for the map option.
+
+E: Processors part option and grid style are incompatible
+
+Cannot use gstyle numa or custom with the part option.
+
+*/

src/comm_tiled.cpp

@@ -0,0 +1,210 @@
+/* ----------------------------------------------------------------------
+   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.
+------------------------------------------------------------------------- */
+
+#include "lmptype.h"
+#include "comm_tiled.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+enum{SINGLE,MULTI};               // same as in Comm
+
+/* ---------------------------------------------------------------------- */
+
+CommTiled::CommTiled(LAMMPS *lmp) : Comm(lmp)
+{
+  style = 1;
+  layout = 0;
+
+  error->all(FLERR,"Comm_style tiled is not yet supported");
+}
+
+/* ---------------------------------------------------------------------- */
+
+CommTiled::~CommTiled()
+{
+}
+
+/* ---------------------------------------------------------------------- */
+
+void CommTiled::init()
+{
+}
+
+/* ----------------------------------------------------------------------
+   setup spatial-decomposition communication patterns
+   function of neighbor cutoff(s) & cutghostuser & current box size
+   single mode sets slab boundaries (slablo,slabhi) based on max cutoff
+   multi mode sets type-dependent slab boundaries (multilo,multihi)
+------------------------------------------------------------------------- */
+
+void CommTiled::setup()
+{
+}
+
+/* ----------------------------------------------------------------------
+   forward communication of atom coords every timestep
+   other per-atom attributes may also be sent via pack/unpack routines
+------------------------------------------------------------------------- */
+
+void CommTiled::forward_comm(int dummy)
+{
+}
+
+/* ----------------------------------------------------------------------
+   reverse communication of forces on atoms every timestep
+   other per-atom attributes may also be sent via pack/unpack routines
+------------------------------------------------------------------------- */
+
+void CommTiled::reverse_comm()
+{
+}
+
+/* ----------------------------------------------------------------------
+   exchange: move atoms to correct processors
+   atoms exchanged with all 6 stencil neighbors
+   send out atoms that have left my box, receive ones entering my box
+   atoms will be lost if not inside some proc's box
+     can happen if atom moves outside of non-periodic bounary
+     or if atom moves more than one proc away
+   this routine called before every reneighboring
+   for triclinic, atoms must be in lamda coords (0-1) before exchange is called
+------------------------------------------------------------------------- */
+
+void CommTiled::exchange()
+{
+}
+
+/* ----------------------------------------------------------------------
+   borders: list nearby atoms to send to neighboring procs at every timestep
+   one list is created for every swap that will be made
+   as list is made, actually do swaps
+   this does equivalent of a communicate, so don't need to explicitly
+     call communicate routine on reneighboring timestep
+   this routine is called before every reneighboring
+   for triclinic, atoms must be in lamda coords (0-1) before borders is called
+------------------------------------------------------------------------- */
+
+void CommTiled::borders()
+{
+}
+
+/* ----------------------------------------------------------------------
+   forward communication invoked by a Pair
+------------------------------------------------------------------------- */
+
+void CommTiled::forward_comm_pair(Pair *pair)
+{
+}
+
+/* ----------------------------------------------------------------------
+   reverse communication invoked by a Pair
+------------------------------------------------------------------------- */
+
+void CommTiled::reverse_comm_pair(Pair *pair)
+{
+}
+
+/* ----------------------------------------------------------------------
+   forward communication invoked by a Fix
+   n = constant number of datums per atom
+------------------------------------------------------------------------- */
+
+void CommTiled::forward_comm_fix(Fix *fix)
+{
+}
+
+/* ----------------------------------------------------------------------
+   reverse communication invoked by a Fix
+   n = constant number of datums per atom
+------------------------------------------------------------------------- */
+
+void CommTiled::reverse_comm_fix(Fix *fix)
+{
+}
+
+/* ----------------------------------------------------------------------
+   forward communication invoked by a Fix
+   n = total datums for all atoms, allows for variable number/atom
+------------------------------------------------------------------------- */
+
+void CommTiled::forward_comm_variable_fix(Fix *fix)
+{
+}
+
+/* ----------------------------------------------------------------------
+   reverse communication invoked by a Fix
+   n = total datums for all atoms, allows for variable number/atom
+------------------------------------------------------------------------- */
+
+void CommTiled::reverse_comm_variable_fix(Fix *fix)
+{
+}
+
+/* ----------------------------------------------------------------------
+   forward communication invoked by a Compute
+------------------------------------------------------------------------- */
+
+void CommTiled::forward_comm_compute(Compute *compute)
+{
+}
+
+/* ----------------------------------------------------------------------
+   reverse communication invoked by a Compute
+------------------------------------------------------------------------- */
+
+void CommTiled::reverse_comm_compute(Compute *compute)
+{
+}
+
+/* ----------------------------------------------------------------------
+   forward communication invoked by a Dump
+------------------------------------------------------------------------- */
+
+void CommTiled::forward_comm_dump(Dump *dump)
+{
+}
+
+/* ----------------------------------------------------------------------
+   reverse communication invoked by a Dump
+------------------------------------------------------------------------- */
+
+void CommTiled::reverse_comm_dump(Dump *dump)
+{
+}
+
+/* ----------------------------------------------------------------------
+   forward communication of N values in array
+------------------------------------------------------------------------- */
+
+void CommTiled::forward_comm_array(int n, double **array)
+{
+}
+
+/* ----------------------------------------------------------------------
+   exchange info provided with all 6 stencil neighbors
+------------------------------------------------------------------------- */
+
+int CommTiled::exchange_variable(int n, double *inbuf, double *&outbuf)
+{
+}
+
+/* ----------------------------------------------------------------------
+   return # of bytes of allocated memory
+------------------------------------------------------------------------- */
+
+bigint CommTiled::memory_usage()
+{
+  bigint bytes = 0;
+  return bytes;
+}

src/comm_tiled.h

@@ -0,0 +1,55 @@
+/* ----------------------------------------------------------------------
+   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.
+------------------------------------------------------------------------- */
+
+#ifndef LMP_COMM_TILED_H
+#define LMP_COMM_TILED_H
+
+#include "comm.h"
+
+namespace LAMMPS_NS {
+
+class CommTiled : public Comm {
+ public:
+  CommTiled(class LAMMPS *);
+  virtual ~CommTiled();
+
+  void init();
+  void setup();                        // setup comm pattern
+  void forward_comm(int dummy = 0);    // forward comm of atom coords
+  void reverse_comm();                 // reverse comm of forces
+  void exchange();                     // move atoms to new procs
+  void borders();                      // setup list of atoms to comm
+
+  void forward_comm_pair(class Pair *);    // forward comm from a Pair
+  void reverse_comm_pair(class Pair *);    // reverse comm from a Pair
+  void forward_comm_fix(class Fix *);      // forward comm from a Fix
+  void reverse_comm_fix(class Fix *);      // reverse comm from a Fix
+  void forward_comm_variable_fix(class Fix *); // variable-size variant
+  void reverse_comm_variable_fix(class Fix *); // variable-size variant
+  void forward_comm_compute(class Compute *);  // forward from a Compute
+  void reverse_comm_compute(class Compute *);  // reverse from a Compute
+  void forward_comm_dump(class Dump *);    // forward comm from a Dump
+  void reverse_comm_dump(class Dump *);    // reverse comm from a Dump
+
+  void forward_comm_array(int, double **);         // forward comm of array
+  int exchange_variable(int, double *, double *&);  // exchange on neigh stencil
+  bigint memory_usage();
+};
+
+}
+
+#endif
+
+/* ERROR/WARNING messages:
+
+*/