mirror of https://github.com/lammps/lammps.git
change purge target in Makefile, also fixed one issue with Make.py
This commit is contained in:
Steve Plimpton
parent
f7b5afee82
commit
b9d0f96a19
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@ -1,5 +1,5 @@
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Run this example as:
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mpirun -np 3 lmp_linux -partition 3x1 -in in.tad
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mpirun -np 3 lmp_g++ -partition 3x1 -in in.tad
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You should be able to use any number of replicas >= 3.
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@ -0,0 +1,266 @@
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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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#include <string.h>
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#include "comm_tiled_kokkos.h"
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#include "comm_brick.h"
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#include "atom_kokkos.h"
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#include "atom_vec.h"
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#include "domain.h"
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#include "force.h"
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#include "pair.h"
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#include "neighbor.h"
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#include "modify.h"
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#include "fix.h"
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#include "compute.h"
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#include "output.h"
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#include "dump.h"
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#include "memory.h"
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#include "error.h"
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#include "atom_masks.h"
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using namespace LAMMPS_NS;
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#define BUFFACTOR 1.5
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#define BUFFACTOR 1.5
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#define BUFMIN 1000
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#define BUFEXTRA 1000
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#define EPSILON 1.0e-6
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#define DELTA_PROCS 16
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enum{SINGLE,MULTI}; // same as in Comm
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enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files
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/* ---------------------------------------------------------------------- */
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CommTiledKokkos::CommTiledKokkos(LAMMPS *lmp) : CommTiled(lmp)
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{
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}
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/* ---------------------------------------------------------------------- */
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//IMPORTANT: we *MUST* pass "*oldcomm" to the Comm initializer here, as
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// the code below *requires* that the (implicit) copy constructor
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// for Comm is run and thus creating a shallow copy of "oldcomm".
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// The call to Comm::copy_arrays() then converts the shallow copy
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// into a deep copy of the class with the new layout.
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CommTiledKokkos::CommTiledKokkos(LAMMPS *lmp, Comm *oldcomm) : CommTiled(lmp,oldcomm)
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{
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}
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/* ---------------------------------------------------------------------- */
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CommTiledKokkos::~CommTiledKokkos()
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{
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}
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/* ---------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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forward communication of atom coords every timestep
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other per-atom attributes may also be sent via pack/unpack routines
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------------------------------------------------------------------------- */
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void CommTiledKokkos::forward_comm(int dummy)
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{
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if (comm_x_only) {
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atomKK->sync(Host,X_MASK);
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atomKK->modified(Host,X_MASK);
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} else if (ghost_velocity) {
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atomKK->sync(Host,X_MASK | V_MASK);
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atomKK->modified(Host,X_MASK | V_MASK);
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} else {
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atomKK->sync(Host,ALL_MASK);
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atomKK->modified(Host,ALL_MASK);
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}
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CommTiled::forward_comm(dummy);
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}
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/* ----------------------------------------------------------------------
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reverse communication of forces on atoms every timestep
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other per-atom attributes may also be sent via pack/unpack routines
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------------------------------------------------------------------------- */
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void CommTiledKokkos::reverse_comm()
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{
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if (comm_f_only)
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atomKK->sync(Host,F_MASK);
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else
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atomKK->sync(Host,ALL_MASK);
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CommTiled::reverse_comm();
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if (comm_f_only)
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atomKK->modified(Host,F_MASK);
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else
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atomKK->modified(Host,ALL_MASK);
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atomKK->sync(Device,ALL_MASK);
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}
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/* ----------------------------------------------------------------------
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exchange: move atoms to correct processors
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atoms exchanged with procs that touch sub-box in each of 3 dims
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send out atoms that have left my box, receive ones entering my box
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atoms will be lost if not inside a touching proc's box
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can happen if atom moves outside of non-periodic bounary
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or if atom moves more than one proc away
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this routine called before every reneighboring
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for triclinic, atoms must be in lamda coords (0-1) before exchange is called
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------------------------------------------------------------------------- */
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void CommTiledKokkos::exchange()
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{
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atomKK->sync(Host,ALL_MASK);
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CommTiled::exchange();
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atomKK->modified(Host,ALL_MASK);
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}
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/* ----------------------------------------------------------------------
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borders: list nearby atoms to send to neighboring procs at every timestep
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one list is created per swap/proc that will be made
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as list is made, actually do communication
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this does equivalent of a forward_comm(), so don't need to explicitly
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call forward_comm() on reneighboring timestep
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this routine is called before every reneighboring
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for triclinic, atoms must be in lamda coords (0-1) before borders is called
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------------------------------------------------------------------------- */
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void CommTiledKokkos::borders()
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{
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atomKK->sync(Host,ALL_MASK);
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CommTiled::borders();
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atomKK->modified(Host,ALL_MASK);
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}
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/* ----------------------------------------------------------------------
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forward communication invoked by a Pair
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nsize used only to set recv buffer limit
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------------------------------------------------------------------------- */
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void CommTiledKokkos::forward_comm_pair(Pair *pair)
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{
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CommTiled::forward_comm_pair(pair);
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}
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/* ----------------------------------------------------------------------
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reverse communication invoked by a Pair
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nsize used only to set recv buffer limit
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------------------------------------------------------------------------- */
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void CommTiledKokkos::reverse_comm_pair(Pair *pair)
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{
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CommTiled::reverse_comm_pair(pair);
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}
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/* ----------------------------------------------------------------------
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forward communication invoked by a Fix
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size/nsize used only to set recv buffer limit
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size = 0 (default) -> use comm_forward from Fix
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size > 0 -> Fix passes max size per atom
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the latter is only useful if Fix does several comm modes,
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some are smaller than max stored in its comm_forward
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------------------------------------------------------------------------- */
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void CommTiledKokkos::forward_comm_fix(Fix *fix, int size)
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{
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CommTiled::forward_comm_fix(fix,size);
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}
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/* ----------------------------------------------------------------------
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reverse communication invoked by a Fix
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size/nsize used only to set recv buffer limit
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size = 0 (default) -> use comm_forward from Fix
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size > 0 -> Fix passes max size per atom
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the latter is only useful if Fix does several comm modes,
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some are smaller than max stored in its comm_forward
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------------------------------------------------------------------------- */
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void CommTiledKokkos::reverse_comm_fix(Fix *fix, int size)
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{
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CommTiled::reverse_comm_fix(fix,size);
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}
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/* ----------------------------------------------------------------------
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reverse communication invoked by a Fix with variable size data
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query fix for all pack sizes to insure buf_send is big enough
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handshake sizes before irregular comm to insure buf_recv is big enough
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NOTE: how to setup one big buf recv with correct offsets ??
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------------------------------------------------------------------------- */
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void CommTiledKokkos::reverse_comm_fix_variable(Fix *fix)
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{
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CommTiled::reverse_comm_fix_variable(fix);
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}
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/* ----------------------------------------------------------------------
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forward communication invoked by a Compute
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nsize used only to set recv buffer limit
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------------------------------------------------------------------------- */
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void CommTiledKokkos::forward_comm_compute(Compute *compute)
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{
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CommTiled::forward_comm_compute(compute);
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}
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/* ----------------------------------------------------------------------
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reverse communication invoked by a Compute
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nsize used only to set recv buffer limit
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------------------------------------------------------------------------- */
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void CommTiledKokkos::reverse_comm_compute(Compute *compute)
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{
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CommTiled::reverse_comm_compute(compute);
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}
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/* ----------------------------------------------------------------------
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forward communication invoked by a Dump
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nsize used only to set recv buffer limit
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------------------------------------------------------------------------- */
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void CommTiledKokkos::forward_comm_dump(Dump *dump)
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{
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CommTiled::forward_comm_dump(dump);
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}
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/* ----------------------------------------------------------------------
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reverse communication invoked by a Dump
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nsize used only to set recv buffer limit
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------------------------------------------------------------------------- */
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void CommTiledKokkos::reverse_comm_dump(Dump *dump)
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{
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CommTiled::reverse_comm_dump(dump);
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}
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/* ----------------------------------------------------------------------
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forward communication of Nsize values in per-atom array
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------------------------------------------------------------------------- */
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void CommTiledKokkos::forward_comm_array(int nsize, double **array)
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{
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CommTiled::forward_comm_array(nsize,array);
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}
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/* ----------------------------------------------------------------------
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exchange info provided with all 6 stencil neighbors
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NOTE: this method is currently not used
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------------------------------------------------------------------------- */
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int CommTiledKokkos::exchange_variable(int n, double *inbuf, double *&outbuf)
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{
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CommTiled::exchange_variable(n,inbuf,outbuf);
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}
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@ -0,0 +1,59 @@
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/* -*- c++ -*- ----------------------------------------------------------
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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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#ifndef LMP_COMM_TILED_KOKKOS_H
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#define LMP_COMM_TILED_KOKKOS_H
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#include "comm_tiled.h"
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#include "kokkos_type.h"
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namespace LAMMPS_NS {
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class CommTiledKokkos : public CommTiled {
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public:
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CommTiledKokkos(class LAMMPS *);
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CommTiledKokkos(class LAMMPS *, class Comm *);
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virtual ~CommTiledKokkos();
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void forward_comm(int dummy = 0); // forward comm of atom coords
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void reverse_comm(); // reverse comm of forces
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void exchange(); // move atoms to new procs
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void borders(); // setup list of atoms to comm
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void forward_comm_pair(class Pair *); // forward comm from a Pair
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void reverse_comm_pair(class Pair *); // reverse comm from a Pair
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void forward_comm_fix(class Fix *, int size=0);
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// forward comm from a Fix
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void reverse_comm_fix(class Fix *, int size=0);
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// reverse comm from a Fix
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void reverse_comm_fix_variable(class Fix *);
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// variable size reverse comm from a Fix
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void forward_comm_compute(class Compute *); // forward from a Compute
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void reverse_comm_compute(class Compute *); // reverse from a Compute
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void forward_comm_dump(class Dump *); // forward comm from a Dump
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void reverse_comm_dump(class Dump *); // reverse comm from a Dump
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void forward_comm_array(int, double **); // forward comm of array
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int exchange_variable(int, double *, double *&); // exchange on neigh stencil
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private:
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};
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}
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#endif
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/* ERROR/WARNING messages:
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*/
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@ -280,15 +280,19 @@ void NeighborKokkos::choose_build(int index, NeighRequest *rq)
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if (rq->kokkos_host != 0) {
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PairPtrHost pb = NULL;
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if (rq->ghost) {
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if (rq->full) pb = &NeighborKokkos::full_bin_kokkos<LMPHostType,0,1>;
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else if (rq->half) &NeighborKokkos::full_bin_kokkos<LMPHostType,1,1>;
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pair_build_host[index] = pb;
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if (rq->full) {
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if (rq->full_cluster) pb = &NeighborKokkos::full_bin_cluster_kokkos<LMPHostType>;
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else pb = &NeighborKokkos::full_bin_kokkos<LMPHostType,0,1>;
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}
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else if (rq->half) pb = &NeighborKokkos::full_bin_kokkos<LMPHostType,1,1>;
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} else {
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if (rq->full) pb = &NeighborKokkos::full_bin_kokkos<LMPHostType,0,0>;
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if (rq->full) {
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if (rq->full_cluster) pb = &NeighborKokkos::full_bin_cluster_kokkos<LMPHostType>;
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else pb = &NeighborKokkos::full_bin_kokkos<LMPHostType,0,0>;
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}
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else if (rq->half) pb = &NeighborKokkos::full_bin_kokkos<LMPHostType,1,0>;
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pair_build_host[index] = pb;
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}
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return;
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pair_build_host[index] = pb;
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}
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if (rq->kokkos_device != 0) {
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PairPtrDevice pb = NULL;
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70
src/Make.py
70
src/Make.py
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@ -26,7 +26,8 @@ libclasses = ("atc","awpmd","colvars","cuda","gpu","h5md",
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buildclasses = ("intel","kokkos")
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makeclasses = ("cc","flags","mpi","fft","jpg","png")
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setargs = ("gzip","#gzip","ffmpeg","#ffmpeg","smallbig","bigbig","smallsmall","exceptions","#exceptions")
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setargs = ("gzip","#gzip","ffmpeg","#ffmpeg","smallbig","bigbig",
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"smallsmall","exceptions","#exceptions")
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actionargs = ("lib-all","file","clean","exe")
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gpubuildflag = 0
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@ -85,7 +86,8 @@ def switch2str(switches,switch_order):
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def compile_check(compiler,ccflags,warn):
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open("tmpauto.cpp",'w').write("int main(int, char **) {}\n")
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tmp = "%s %s -c tmpauto.cpp" % (compiler,ccflags)
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try: txt = subprocess.check_output(tmp,stderr=subprocess.STDOUT,shell=True).decode()
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try: txt = subprocess.check_output(tmp,stderr=subprocess.STDOUT,
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shell=True).decode()
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except subprocess.CalledProcessError as e: txt = e.output
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flag = 1
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if txt or not os.path.isfile("tmpauto.o"):
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@ -105,7 +107,8 @@ def compile_check(compiler,ccflags,warn):
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def link_check(linker,linkflags,libs,warn):
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open("tmpauto.cpp",'w').write("int main(int, char **) {}\n")
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tmp = "%s %s -o tmpauto tmpauto.cpp %s" % (linker,linkflags,libs)
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try: txt = subprocess.check_output(tmp,stderr=subprocess.STDOUT,shell=True).decode()
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try: txt = subprocess.check_output(tmp,stderr=subprocess.STDOUT,
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shell=True).decode()
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except subprocess.CalledProcessError as e: txt = e.output
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flag = 1
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if txt or not os.path.isfile("tmpauto"):
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@ -532,7 +535,8 @@ class Actions(object):
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if caller == "file" or "file" not in self.alist:
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# make certain that 'MAKE/MINE' folder exists.
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subprocess.check_output("mkdir -p %s/MAKE/MINE" % dir.src,stderr=subprocess.STDOUT,shell=True)
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subprocess.check_output("mkdir -p %s/MAKE/MINE" % dir.src,
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stderr=subprocess.STDOUT,shell=True)
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make.write("%s/MAKE/MINE/Makefile.auto" % dir.src,1)
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print("Created src/MAKE/MINE/Makefile.auto")
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@ -859,9 +863,12 @@ class Packages(object):
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if self.plist: print("Installing packages ...")
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for one in self.plist:
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if one == "orig": continue
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subprocess.check_output("cd %s; make %s" % (dir.src,one),stderr=subprocess.STDOUT,shell=True)
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subprocess.check_output("cd %s; make %s" % (dir.src,one),
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stderr=subprocess.STDOUT,shell=True)
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if self.plist and verbose:
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txt = subprocess.check_output("cd %s; make ps" % dir.src,stderr=subprocess.STDOUT,shell=True).decode()
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txt = subprocess.check_output("cd %s; make ps" % dir.src,
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stderr=subprocess.STDOUT,
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shell=True).decode()
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print("Package status after installation:")
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print(txt)
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@ -871,12 +878,16 @@ class Packages(object):
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def uninstall(self):
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if not self.plist or self.plist[-1] != "orig": return
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print("Restoring packages to original state ...")
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subprocess.check_output("cd %s; make no-all" % dir.src,stderr=subprocess.STDOUT,shell=True)
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subprocess.check_output("cd %s; make no-all" % dir.src,
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stderr=subprocess.STDOUT,shell=True)
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for one in self.all:
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if self.original[one]:
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subprocess.check_output("cd %s; make yes-%s" % (dir.src,one),stderr=subprocess.STDOUT,shell=True)
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subprocess.check_output("cd %s; make yes-%s" % (dir.src,one),
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stderr=subprocess.STDOUT,shell=True)
|
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if verbose:
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txt = subprocess.check_output("cd %s; make ps" % dir.src,stderr=subprocess.STDOUT,shell=True).decode()
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txt = subprocess.check_output("cd %s; make ps" % dir.src,
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stderr=subprocess.STDOUT,
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shell=True).decode()
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print("Restored package status:")
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print(txt)
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|
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@ -970,7 +981,8 @@ class Settings(object):
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def help(self):
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return """
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||||
-s set1 set2 ...
|
||||
possible settings = gzip #gzip ffmpeg #ffmpeg smallbig bigbig smallsmall exceptions #exceptions
|
||||
possible settings = gzip #gzip ffmpeg #ffmpeg
|
||||
smallbig bigbig smallsmall exceptions #exceptions
|
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alter LAMMPS ifdef settings in Makefile.auto
|
||||
only happens if new Makefile.auto is created by use of "file" action
|
||||
gzip and #gzip turn on/off LAMMPS_GZIP setting
|
||||
|
|
@ -1059,7 +1071,8 @@ class ATC(object):
|
|||
make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
|
||||
make.write("%s/Makefile.auto" % libdir)
|
||||
|
||||
subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,stderr=subprocess.STDOUT,shell=True)
|
||||
subprocess.check_output("cd %s; make -f Makefile.auto clean" %
|
||||
libdir,stderr=subprocess.STDOUT,shell=True)
|
||||
if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
|
||||
else: txt = "cd %s; make -f Makefile.auto" % libdir
|
||||
|
||||
|
|
@ -1110,7 +1123,8 @@ class AWPMD(object):
|
|||
make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
|
||||
make.write("%s/Makefile.auto" % libdir)
|
||||
|
||||
subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,stderr=subprocess.STDOUT,shell=True)
|
||||
subprocess.check_output("cd %s; make -f Makefile.auto clean" %
|
||||
libdir,stderr=subprocess.STDOUT,shell=True)
|
||||
if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
|
||||
else: txt = "cd %s; make -f Makefile.auto" % libdir
|
||||
|
||||
|
|
@ -1161,7 +1175,8 @@ class COLVARS(object):
|
|||
make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
|
||||
make.write("%s/Makefile.auto" % libdir)
|
||||
|
||||
subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,stderr=subprocess.STDOUT,shell=True)
|
||||
subprocess.check_output("cd %s; make -f Makefile.auto clean" %
|
||||
libdir,stderr=subprocess.STDOUT,shell=True)
|
||||
if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
|
||||
else: txt = "cd %s; make -f Makefile.auto" % libdir
|
||||
|
||||
|
|
@ -1213,7 +1228,8 @@ class CUDA(object):
|
|||
|
||||
def build(self):
|
||||
libdir = dir.lib + "/cuda"
|
||||
subprocess.check_output("cd %s; make clean" % libdir,stderr=subprocess.STDOUT,shell=True)
|
||||
subprocess.check_output("cd %s; make clean" % libdir,
|
||||
stderr=subprocess.STDOUT,shell=True)
|
||||
if self.mode == "double": n = 2
|
||||
elif self.mode == "mixed": n = 3
|
||||
elif self.mode == "single": n = 1
|
||||
|
|
@ -1308,7 +1324,8 @@ class GPU(object):
|
|||
make = "make"
|
||||
if "shannon" == platform.node(): make = "srun make"
|
||||
|
||||
subprocess.check_output("cd %s; %s -f Makefile.auto clean" % (libdir,make),stderr=subprocess.STDOUT,shell=True)
|
||||
subprocess.check_output("cd %s; %s -f Makefile.auto clean" %
|
||||
(libdir,make),stderr=subprocess.STDOUT,shell=True)
|
||||
if jmake: txt = "cd %s; %s -j %d -f Makefile.auto" % (libdir,make,jmake.n)
|
||||
else: txt = "cd %s; %s -f Makefile.auto" % (libdir,make)
|
||||
|
||||
|
|
@ -1359,7 +1376,8 @@ class H5MD(object):
|
|||
make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
|
||||
make.write("%s/Makefile.auto" % libdir)
|
||||
|
||||
subprocess.check_output("cd %s; make clean" % libdir,stderr=subprocess.STDOUT,shell=True)
|
||||
subprocess.check_output("cd %s; make clean" % libdir,
|
||||
stderr=subprocess.STDOUT,shell=True)
|
||||
txt = "cd %s; make" % libdir
|
||||
|
||||
# if verbose, print output as build proceeds, else only print if fails
|
||||
|
|
@ -1409,7 +1427,8 @@ class MEAM(object):
|
|||
make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
|
||||
make.write("%s/Makefile.auto" % libdir)
|
||||
|
||||
subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,stderr=subprocess.STDOUT,shell=True)
|
||||
subprocess.check_output("cd %s; make -f Makefile.auto clean" %
|
||||
libdir,stderr=subprocess.STDOUT,shell=True)
|
||||
# do not use -j for MEAM build, parallel build does not work
|
||||
txt = "cd %s; make -f Makefile.auto" % libdir
|
||||
|
||||
|
|
@ -1460,7 +1479,8 @@ class POEMS(object):
|
|||
make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
|
||||
make.write("%s/Makefile.auto" % libdir)
|
||||
|
||||
subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,stderr=subprocess.STDOUT,shell=True)
|
||||
subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,
|
||||
stderr=subprocess.STDOUT,shell=True)
|
||||
if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
|
||||
else: txt = "cd %s; make -f Makefile.auto" % libdir
|
||||
|
||||
|
|
@ -1506,9 +1526,10 @@ class PYTHON(object):
|
|||
libdir = dir.lib + "/python"
|
||||
if self.lammpsflag:
|
||||
subprocess.check_output("cd %s; cp Makefile.lammps.%s Makefile.lammps" %
|
||||
(libdir,self.lammps))
|
||||
(libdir,self.lammps))
|
||||
if not os.path.isfile("%s/Makefile.lammps.%s" % (libdir,self.lammps)):
|
||||
error("Unsuccessful creation of lib/python/Makefile.lammps.%s file" % self.lammps)
|
||||
error("Unsuccessful creation of lib/python/Makefile.lammps.%s file" %
|
||||
self.lammps)
|
||||
else: print("Created lib/python/Makefile.lammps file")
|
||||
|
||||
# QMMM lib
|
||||
|
|
@ -1546,7 +1567,8 @@ class QMMM(object):
|
|||
make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
|
||||
make.write("%s/Makefile.auto" % libdir)
|
||||
|
||||
subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,stderr=subprocess.STDOUT,shell=True)
|
||||
subprocess.check_output("cd %s; make -f Makefile.auto clean" %
|
||||
libdir,stderr=subprocess.STDOUT,shell=True)
|
||||
if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
|
||||
else: txt = "cd %s; make -f Makefile.auto" % libdir
|
||||
|
||||
|
|
@ -1597,7 +1619,8 @@ class REAX(object):
|
|||
make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
|
||||
make.write("%s/Makefile.auto" % libdir)
|
||||
|
||||
commands.getoutput("cd %s; make -f Makefile.auto clean" % libdir)
|
||||
cmd = "cd %s; make -f Makefile.auto clean" % libdir
|
||||
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
|
||||
if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
|
||||
else: txt = "cd %s; make -f Makefile.auto" % libdir
|
||||
|
||||
|
|
@ -1643,7 +1666,8 @@ class VORONOI(object):
|
|||
if not self.install: return
|
||||
libdir = dir.lib + "/voronoi"
|
||||
cmd = "cd %s; python install.py %s" % (libdir,self.install)
|
||||
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True).decode()
|
||||
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,
|
||||
shell=True).decode()
|
||||
if verbose: print(txt)
|
||||
print("Created lib/voronoi library")
|
||||
|
||||
|
|
|
|||
|
|
@ -92,7 +92,7 @@ help:
|
|||
@echo 'make package-update (pu) replace src files with updated package files'
|
||||
@echo 'make package-overwrite replace package files with src files'
|
||||
@echo 'make package-diff (pd) diff src files against package files'
|
||||
@echo 'make package-purge purge obsolete copies of package sources'
|
||||
@echo 'make purge purge obsolete copies of source files'
|
||||
@echo ''
|
||||
@echo 'make machine build LAMMPS for machine'
|
||||
@echo 'make mode=lib machine build LAMMPS as static lib for machine'
|
||||
|
|
@ -314,7 +314,7 @@ package-diff pd:
|
|||
@echo ''
|
||||
@for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p diff; done
|
||||
|
||||
package-purge: Purge.list
|
||||
purge: Purge.list
|
||||
@echo 'Purging obsolete and auto-generated source files'
|
||||
@for f in `grep -v '#' Purge.list` ; \
|
||||
do test -f $$f && rm $$f && echo $$f || : ; \
|
||||
|
|
|
|||
|
|
@ -348,7 +348,7 @@ void PairReaxC::init_style( )
|
|||
|
||||
int iqeq;
|
||||
for (iqeq = 0; iqeq < modify->nfix; iqeq++)
|
||||
if (strcmp(modify->fix[iqeq]->style,"qeq/reax") == 0) break;
|
||||
if (strstr(modify->fix[iqeq]->style,"qeq/reax")) break;
|
||||
if (iqeq == modify->nfix && qeqflag == 1)
|
||||
error->all(FLERR,"Pair reax/c requires use of fix qeq/reax");
|
||||
|
||||
|
|
|
|||
|
|
@ -45,9 +45,6 @@ enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files
|
|||
|
||||
CommTiled::CommTiled(LAMMPS *lmp) : Comm(lmp)
|
||||
{
|
||||
if (lmp->kokkos)
|
||||
error->all(FLERR,"KOKKOS package does not yet support comm_style tiled");
|
||||
|
||||
style = 1;
|
||||
layout = LAYOUT_UNIFORM;
|
||||
pbc_flag = NULL;
|
||||
|
|
@ -63,9 +60,6 @@ CommTiled::CommTiled(LAMMPS *lmp) : Comm(lmp)
|
|||
|
||||
CommTiled::CommTiled(LAMMPS *lmp, Comm *oldcomm) : Comm(*oldcomm)
|
||||
{
|
||||
if (lmp->kokkos)
|
||||
error->all(FLERR,"KOKKOS package does not yet support comm_style tiled");
|
||||
|
||||
style = 1;
|
||||
layout = oldcomm->layout;
|
||||
Comm::copy_arrays(oldcomm);
|
||||
|
|
|
|||
|
|
@ -26,26 +26,26 @@ class CommTiled : public Comm {
|
|||
|
||||
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
|
||||
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
|
||||
|
||||
void forward_comm_pair(class Pair *); // forward comm from a Pair
|
||||
void reverse_comm_pair(class Pair *); // reverse comm from a Pair
|
||||
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 *, int size=0);
|
||||
// forward comm from a Fix
|
||||
virtual void reverse_comm_fix(class Fix *, int size=0);
|
||||
// reverse comm from a Fix
|
||||
virtual void reverse_comm_fix_variable(class Fix *);
|
||||
// variable size reverse comm from a Fix
|
||||
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
|
||||
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 void forward_comm_array(int, double **); // forward comm of array
|
||||
virtual int exchange_variable(int, double *, double *&); // exchange on neigh stencil
|
||||
|
||||
void coord2proc_setup();
|
||||
int coord2proc(double *, int &, int &, int &);
|
||||
|
|
|
|||
Loading…
Reference in New Issue