From 0553f4af2b9432eb17351a4a2c1c39b2d15bc703 Mon Sep 17 00:00:00 2001
From: sjplimp
Date: Wed, 2 Jul 2014 14:30:06 +0000
Subject: [PATCH 01/19] git-svn-id:
svn://svn.icms.temple.edu/lammps-ro/trunk@12168
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
tools/python/README | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/tools/python/README b/tools/python/README
index d895573628..61f6cfe7df 100644
--- a/tools/python/README
+++ b/tools/python/README
@@ -33,8 +33,8 @@ for details and download info:
www.sandia.gov/~sjplimp/pizza.html
The tools in the Pizza.py src directory are identical to those in the
-pizza sub-directory of lammps/tools/python. The header section of the
-tool files lists all the functionality that tool supports.
+pizza sub-directory of lammps/tools/python. The header section of
+each tool file lists all the functionality that tool supports.
To use all the features of Pizza.py modules, you need to be familiar
with Python syntax. You can then modify the scripts to invoke
From b5d89cd7689e78a94f9d5ee00052438dff5535af Mon Sep 17 00:00:00 2001
From: sjplimp
Date: Wed, 2 Jul 2014 20:53:37 +0000
Subject: [PATCH 02/19] git-svn-id:
svn://svn.icms.temple.edu/lammps-ro/trunk@12169
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
lib/gpu/lal_coul.cpp | 166 +++++++++++++++++++++++++
lib/gpu/lal_coul.cu | 211 +++++++++++++++++++++++++++++++
lib/gpu/lal_coul.h | 83 +++++++++++++
lib/gpu/lal_coul_debye.cpp | 167 +++++++++++++++++++++++++
lib/gpu/lal_coul_debye.cu | 220 +++++++++++++++++++++++++++++++++
lib/gpu/lal_coul_debye.h | 84 +++++++++++++
lib/gpu/lal_coul_debye_ext.cpp | 143 +++++++++++++++++++++
lib/gpu/lal_coul_ext.cpp | 143 +++++++++++++++++++++
8 files changed, 1217 insertions(+)
create mode 100644 lib/gpu/lal_coul.cpp
create mode 100644 lib/gpu/lal_coul.cu
create mode 100644 lib/gpu/lal_coul.h
create mode 100644 lib/gpu/lal_coul_debye.cpp
create mode 100644 lib/gpu/lal_coul_debye.cu
create mode 100644 lib/gpu/lal_coul_debye.h
create mode 100644 lib/gpu/lal_coul_debye_ext.cpp
create mode 100644 lib/gpu/lal_coul_ext.cpp
diff --git a/lib/gpu/lal_coul.cpp b/lib/gpu/lal_coul.cpp
new file mode 100644
index 0000000000..53fb3dae82
--- /dev/null
+++ b/lib/gpu/lal_coul.cpp
@@ -0,0 +1,166 @@
+/***************************************************************************
+ coul.cpp
+ -------------------
+ Trung Dac Nguyen
+
+ Class for acceleration of the coul/cut pair style.
+
+ __________________________________________________________________________
+ This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+ __________________________________________________________________________
+
+ begin :
+ email : ndtrung@umich.edu
+ ***************************************************************************/
+
+#if defined(USE_OPENCL)
+#include "coul_cl.h"
+#elif defined(USE_CUDART)
+const char *coul=0;
+#else
+#include "coul_cubin.h"
+#endif
+
+#include "lal_coul.h"
+#include
+using namespace LAMMPS_AL;
+#define CoulT Coul
+
+extern Device device;
+
+template
+CoulT::Coul() : BaseCharge(),
+ _allocated(false) {
+}
+
+template
+CoulT::~Coul() {
+ clear();
+}
+
+template
+int CoulT::bytes_per_atom(const int max_nbors) const {
+ return this->bytes_per_atom_atomic(max_nbors);
+}
+
+template
+int CoulT::init(const int ntypes, double **host_scale, double **host_cutsq,
+ double *host_special_coul, const int nlocal,
+ const int nall, const int max_nbors,
+ const int maxspecial, const double cell_size,
+ const double gpu_split, FILE *_screen,
+ const double qqrd2e) {
+ int success;
+ success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split,
+ _screen,coul,"k_coul");
+ if (success!=0)
+ return success;
+
+ // If atom type constants fit in shared memory use fast kernel
+ int lj_types=ntypes;
+ shared_types=false;
+ int max_shared_types=this->device->max_shared_types();
+ if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) {
+ lj_types=max_shared_types;
+ shared_types=true;
+ }
+ _lj_types=lj_types;
+
+ // Allocate a host write buffer for data initialization
+ UCL_H_Vec host_write(lj_types*lj_types*32,*(this->ucl_device),
+ UCL_WRITE_ONLY);
+
+ for (int i=0; iucl_device),UCL_READ_ONLY);
+ this->atom->type_pack1(ntypes,lj_types,scale,host_write,host_scale);
+
+ cutsq.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
+ this->atom->type_pack1(ntypes,lj_types,cutsq,host_write,host_cutsq);
+
+ sp_cl.alloc(4,*(this->ucl_device),UCL_READ_ONLY);
+ for (int i=0; i<4; i++) {
+ host_write[i]=host_special_coul[i];
+ }
+ ucl_copy(sp_cl,host_write,4,false);
+
+ _qqrd2e=qqrd2e;
+
+ _allocated=true;
+ this->_max_bytes=cutsq.row_bytes()+sp_cl.row_bytes();
+ return 0;
+}
+
+template
+void CoulT::reinit(const int ntypes, double **host_scale) {
+ // Allocate a host write buffer for data initialization
+ UCL_H_Vec host_write(_lj_types*_lj_types*32,*(this->ucl_device),
+ UCL_WRITE_ONLY);
+
+ for (int i=0; i<_lj_types*_lj_types; i++)
+ host_write[i]=0.0;
+
+ this->atom->type_pack1(ntypes,_lj_types,scale,host_write,host_scale);
+}
+
+template
+void CoulT::clear() {
+ if (!_allocated)
+ return;
+ _allocated=false;
+
+ scale.clear();
+ cutsq.clear();
+ sp_cl.clear();
+ this->clear_atomic();
+}
+
+template
+double CoulT::host_memory_usage() const {
+ return this->host_memory_usage_atomic()+sizeof(Coul);
+}
+
+// ---------------------------------------------------------------------------
+// Calculate energies, forces, and torques
+// ---------------------------------------------------------------------------
+template
+void CoulT::loop(const bool _eflag, const bool _vflag) {
+ // Compute the block size and grid size to keep all cores busy
+ const int BX=this->block_size();
+ int eflag, vflag;
+ if (_eflag)
+ eflag=1;
+ else
+ eflag=0;
+
+ if (_vflag)
+ vflag=1;
+ else
+ vflag=0;
+
+ int GX=static_cast(ceil(static_cast(this->ans->inum())/
+ (BX/this->_threads_per_atom)));
+
+ int ainum=this->ans->inum();
+ int nbor_pitch=this->nbor->nbor_pitch();
+ this->time_pair.start();
+ if (shared_types) {
+ this->k_pair_fast.set_size(GX,BX);
+ this->k_pair_fast.run(&this->atom->x, &scale, &sp_cl,
+ &this->nbor->dev_nbor, &this->_nbor_data->begin(),
+ &this->ans->force, &this->ans->engv, &eflag,
+ &vflag, &ainum, &nbor_pitch, &this->atom->q,
+ &cutsq, &_qqrd2e, &this->_threads_per_atom);
+ } else {
+ this->k_pair.set_size(GX,BX);
+ this->k_pair.run(&this->atom->x, &scale, &_lj_types, &sp_cl,
+ &this->nbor->dev_nbor, &this->_nbor_data->begin(),
+ &this->ans->force, &this->ans->engv,
+ &eflag, &vflag, &ainum, &nbor_pitch, &this->atom->q,
+ &cutsq, &_qqrd2e, &this->_threads_per_atom);
+ }
+ this->time_pair.stop();
+}
+
+template class Coul;
diff --git a/lib/gpu/lal_coul.cu b/lib/gpu/lal_coul.cu
new file mode 100644
index 0000000000..7f8b9af6a0
--- /dev/null
+++ b/lib/gpu/lal_coul.cu
@@ -0,0 +1,211 @@
+// **************************************************************************
+// coul.cu
+// -------------------
+// Trung Dac Nguyen
+//
+// Device code for acceleration of the coul/cut pair style
+//
+// __________________________________________________________________________
+// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+// __________________________________________________________________________
+//
+// begin :
+// email : ndtrung@umich.edu
+// ***************************************************************************/
+
+#ifdef NV_KERNEL
+
+#include "lal_aux_fun1.h"
+#ifndef _DOUBLE_DOUBLE
+texture pos_tex;
+texture q_tex;
+#else
+texture pos_tex;
+texture q_tex;
+#endif
+
+#else
+#define pos_tex x_
+#define q_tex q_
+#endif
+
+__kernel void k_coul(const __global numtyp4 *restrict x_,
+ const __global numtyp *restrict scale,
+ const int lj_types,
+ const __global numtyp *restrict sp_cl_in,
+ const __global int *dev_nbor,
+ const __global int *dev_packed,
+ __global acctyp4 *restrict ans,
+ __global acctyp *restrict engv,
+ const int eflag, const int vflag, const int inum,
+ const int nbor_pitch,
+ const __global numtyp *restrict q_,
+ const __global numtyp *restrict cutsq,
+ const numtyp qqrd2e, const int t_per_atom) {
+ int tid, ii, offset;
+ atom_info(t_per_atom,ii,tid,offset);
+
+ __local numtyp sp_cl[8];
+ sp_cl[0]=sp_cl_in[0];
+ sp_cl[1]=sp_cl_in[1];
+ sp_cl[2]=sp_cl_in[2];
+ sp_cl[3]=sp_cl_in[3];
+
+ acctyp energy=(acctyp)0;
+ acctyp e_coul=(acctyp)0;
+ acctyp4 f;
+ f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
+ acctyp virial[6];
+ for (int i=0; i<6; i++)
+ virial[i]=(acctyp)0;
+
+ if (ii0) {
+ e_coul += forcecoul;
+ }
+ if (vflag>0) {
+ virial[0] += delx*delx*force;
+ virial[1] += dely*dely*force;
+ virial[2] += delz*delz*force;
+ virial[3] += delx*dely*force;
+ virial[4] += delx*delz*force;
+ virial[5] += dely*delz*force;
+ }
+ }
+
+ } // for nbor
+ store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag,
+ vflag,ans,engv);
+ } // if ii
+}
+
+__kernel void k_coul_fast(const __global numtyp4 *restrict x_,
+ const __global numtyp *restrict scale,
+ const __global numtyp *restrict sp_cl_in,
+ const __global int *dev_nbor,
+ const __global int *dev_packed,
+ __global acctyp4 *restrict ans,
+ __global acctyp *restrict engv,
+ const int eflag, const int vflag, const int inum,
+ const int nbor_pitch,
+ const __global numtyp *restrict q_,
+ const __global numtyp *restrict _cutsq,
+ const numtyp qqrd2e, const int t_per_atom) {
+ int tid, ii, offset;
+ atom_info(t_per_atom,ii,tid,offset);
+
+ __local numtyp cutsq[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
+ __local numtyp sp_cl[4];
+ if (tid<4)
+ sp_cl[tid]=sp_cl_in[tid];
+ if (tid0) {
+ e_coul += forcecoul;
+ }
+ if (vflag>0) {
+ virial[0] += delx*delx*force;
+ virial[1] += dely*dely*force;
+ virial[2] += delz*delz*force;
+ virial[3] += delx*dely*force;
+ virial[4] += delx*delz*force;
+ virial[5] += dely*delz*force;
+ }
+ }
+
+ } // for nbor
+ store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag,
+ vflag,ans,engv);
+ } // if ii
+}
+
diff --git a/lib/gpu/lal_coul.h b/lib/gpu/lal_coul.h
new file mode 100644
index 0000000000..4374abd80d
--- /dev/null
+++ b/lib/gpu/lal_coul.h
@@ -0,0 +1,83 @@
+/***************************************************************************
+ coul.h
+ -------------------
+ Trung Dac Nguyen
+
+ Class for acceleration of the coul/cut pair style.
+
+ __________________________________________________________________________
+ This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+ __________________________________________________________________________
+
+ begin :
+ email : ndtrung@umich.edu
+ ***************************************************************************/
+
+#ifndef LAL_COUL_H
+#define LAL_COUL_H
+
+#include "lal_base_charge.h"
+
+namespace LAMMPS_AL {
+
+template
+class Coul : public BaseCharge {
+ public:
+ Coul();
+ ~Coul();
+
+ /// Clear any previous data and set up for a new LAMMPS run
+ /** \param max_nbors initial number of rows in the neighbor matrix
+ * \param cell_size cutoff + skin
+ * \param gpu_split fraction of particles handled by device
+ *
+ * Returns:
+ * - 0 if successfull
+ * - -1 if fix gpu not found
+ * - -3 if there is an out of memory error
+ * - -4 if the GPU library was not compiled for GPU
+ * - -5 Double precision is not supported on card **/
+ int init(const int ntypes, double **host_scale,
+ double **host_cutsq, double *host_special_coul,
+ const int nlocal, const int nall, const int max_nbors,
+ const int maxspecial, const double cell_size,
+ const double gpu_split, FILE *screen, const double qqrd2e);
+
+ /// Send updated coeffs from host to device (to be compatible with fix adapt)
+ void reinit(const int ntypes, double **host_scale);
+
+ /// Clear all host and device data
+ /** \note This is called at the beginning of the init() routine **/
+ void clear();
+
+ /// Returns memory usage on device per atom
+ int bytes_per_atom(const int max_nbors) const;
+
+ /// Total host memory used by library for pair style
+ double host_memory_usage() const;
+
+ // --------------------------- TYPE DATA --------------------------
+
+ /// cutsq
+ UCL_D_Vec scale;
+ /// cutsq
+ UCL_D_Vec cutsq;
+ /// Special Coul values [0-3]
+ UCL_D_Vec sp_cl;
+
+ /// If atom type constants fit in shared memory, use fast kernels
+ bool shared_types;
+
+ /// Number of atom types
+ int _lj_types;
+
+ numtyp _qqrd2e;
+
+ private:
+ bool _allocated;
+ void loop(const bool _eflag, const bool _vflag);
+};
+
+}
+
+#endif
diff --git a/lib/gpu/lal_coul_debye.cpp b/lib/gpu/lal_coul_debye.cpp
new file mode 100644
index 0000000000..990dff6db9
--- /dev/null
+++ b/lib/gpu/lal_coul_debye.cpp
@@ -0,0 +1,167 @@
+/***************************************************************************
+ coul_debye.cpp
+ -------------------
+ Trung Dac Nguyen
+
+ Class for acceleration of the coul/debye pair style.
+
+ __________________________________________________________________________
+ This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+ __________________________________________________________________________
+
+ begin :
+ email : ndtrung@umich.edu
+ ***************************************************************************/
+
+#ifdef USE_OPENCL
+#include "coul_debye_cl.h"
+#elif defined(USE_CUDART)
+const char *coul_debye=0;
+#else
+#include "coul_debye_cubin.h"
+#endif
+
+#include "lal_coul_debye.h"
+#include
+using namespace LAMMPS_AL;
+#define CoulDebyeT CoulDebye
+
+extern Device device;
+
+template
+CoulDebyeT::CoulDebye() : BaseCharge(),
+ _allocated(false) {
+}
+
+template
+CoulDebyeT::~CoulDebye() {
+ clear();
+}
+
+template
+int CoulDebyeT::bytes_per_atom(const int max_nbors) const {
+ return this->bytes_per_atom_atomic(max_nbors);
+}
+
+template
+int CoulDebyeT::init(const int ntypes, double **host_scale,
+ double **host_cutsq, double *host_special_coul,
+ const int nlocal, const int nall, const int max_nbors,
+ const int maxspecial, const double cell_size,
+ const double gpu_split, FILE *_screen,
+ const double qqrd2e, const double kappa) {
+ int success;
+ success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split,
+ _screen,coul_debye,"k_coul_debye");
+ if (success!=0)
+ return success;
+
+ // If atom type constants fit in shared memory use fast kernel
+ int lj_types=ntypes;
+ shared_types=false;
+ int max_shared_types=this->device->max_shared_types();
+ if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) {
+ lj_types=max_shared_types;
+ shared_types=true;
+ }
+ _lj_types=lj_types;
+
+ // Allocate a host write buffer for data initialization
+ UCL_H_Vec host_write(lj_types*lj_types*32,*(this->ucl_device),
+ UCL_WRITE_ONLY);
+
+ for (int i=0; iucl_device),UCL_READ_ONLY);
+ this->atom->type_pack1(ntypes,lj_types,scale,host_write,host_scale);
+
+ cutsq.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
+ this->atom->type_pack1(ntypes,lj_types,cutsq,host_write,host_cutsq);
+
+ sp_cl.alloc(4,*(this->ucl_device),UCL_READ_ONLY);
+ for (int i=0; i<4; i++) {
+ host_write[i]=host_special_coul[i];
+ }
+ ucl_copy(sp_cl,host_write,4,false);
+
+ _qqrd2e=qqrd2e;
+ _kappa=kappa;
+
+ _allocated=true;
+ this->_max_bytes=cutsq.row_bytes()+scale.row_bytes()+sp_cl.row_bytes();
+ return 0;
+}
+
+template
+void CoulDebyeT::reinit(const int ntypes, double **host_scale) {
+ // Allocate a host write buffer for data initialization
+ UCL_H_Vec host_write(_lj_types*_lj_types*32,*(this->ucl_device),
+ UCL_WRITE_ONLY);
+
+ for (int i=0; i<_lj_types*_lj_types; i++)
+ host_write[i]=0.0;
+
+ this->atom->type_pack1(ntypes,_lj_types,scale,host_write,host_scale);
+}
+
+template
+void CoulDebyeT::clear() {
+ if (!_allocated)
+ return;
+ _allocated=false;
+
+ scale.clear();
+ cutsq.clear();
+ sp_cl.clear();
+ this->clear_atomic();
+}
+
+template
+double CoulDebyeT::host_memory_usage() const {
+ return this->host_memory_usage_atomic()+sizeof(CoulDebye);
+}
+
+// ---------------------------------------------------------------------------
+// Calculate energies, forces, and torques
+// ---------------------------------------------------------------------------
+template
+void CoulDebyeT::loop(const bool _eflag, const bool _vflag) {
+ // Compute the block size and grid size to keep all cores busy
+ const int BX=this->block_size();
+ int eflag, vflag;
+ if (_eflag)
+ eflag=1;
+ else
+ eflag=0;
+
+ if (_vflag)
+ vflag=1;
+ else
+ vflag=0;
+
+ int GX=static_cast(ceil(static_cast(this->ans->inum())/
+ (BX/this->_threads_per_atom)));
+
+ int ainum=this->ans->inum();
+ int nbor_pitch=this->nbor->nbor_pitch();
+ this->time_pair.start();
+ if (shared_types) {
+ this->k_pair_fast.set_size(GX,BX);
+ this->k_pair_fast.run(&this->atom->x, &scale, &sp_cl,
+ &this->nbor->dev_nbor, &this->_nbor_data->begin(),
+ &this->ans->force, &this->ans->engv, &eflag, &vflag,
+ &ainum, &nbor_pitch, &this->atom->q, &cutsq,
+ &_qqrd2e, &_kappa, &this->_threads_per_atom);
+ } else {
+ this->k_pair.set_size(GX,BX);
+ this->k_pair.run(&this->atom->x, &scale, &_lj_types, &sp_cl,
+ &this->nbor->dev_nbor, &this->_nbor_data->begin(),
+ &this->ans->force, &this->ans->engv, &eflag, &vflag,
+ &ainum, &nbor_pitch, &this->atom->q, &cutsq,
+ &_qqrd2e, &_kappa, &this->_threads_per_atom);
+ }
+ this->time_pair.stop();
+}
+
+template class CoulDebye;
diff --git a/lib/gpu/lal_coul_debye.cu b/lib/gpu/lal_coul_debye.cu
new file mode 100644
index 0000000000..a1c5da34ba
--- /dev/null
+++ b/lib/gpu/lal_coul_debye.cu
@@ -0,0 +1,220 @@
+// **************************************************************************
+// coul_debye.cu
+// -------------------
+// Trung Dac Nguyen
+//
+// Device code for acceleration of the coul/debye pair style
+//
+// __________________________________________________________________________
+// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+// __________________________________________________________________________
+//
+// begin :
+// email : ndtrung@umich.edu
+// ***************************************************************************/
+
+#ifdef NV_KERNEL
+
+#include "lal_aux_fun1.h"
+#ifndef _DOUBLE_DOUBLE
+texture pos_tex;
+texture q_tex;
+#else
+texture pos_tex;
+texture q_tex;
+#endif
+
+#else
+#define pos_tex x_
+#define q_tex q_
+#endif
+
+__kernel void k_coul_debye(const __global numtyp4 *restrict x_,
+ const __global numtyp *restrict scale,
+ const int lj_types,
+ const __global numtyp *restrict sp_cl_in,
+ const __global int *dev_nbor,
+ const __global int *dev_packed,
+ __global acctyp4 *restrict ans,
+ __global acctyp *restrict engv,
+ const int eflag, const int vflag, const int inum,
+ const int nbor_pitch,
+ const __global numtyp *restrict q_ ,
+ const __global numtyp *restrict cutsq,
+ const numtyp qqrd2e, const numtyp kappa,
+ const int t_per_atom) {
+ int tid, ii, offset;
+ atom_info(t_per_atom,ii,tid,offset);
+
+ __local numtyp sp_cl[4];
+ sp_cl[0]=sp_cl_in[0];
+ sp_cl[1]=sp_cl_in[1];
+ sp_cl[2]=sp_cl_in[2];
+ sp_cl[3]=sp_cl_in[3];
+
+ acctyp energy=(acctyp)0;
+ acctyp e_coul=(acctyp)0;
+ acctyp4 f;
+ f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
+ acctyp virial[6];
+ for (int i=0; i<6; i++)
+ virial[i]=(acctyp)0;
+
+ if (ii0) {
+ e_coul+=qqrd2e*scale[mtype]*qtmp*rinv*screening*factor_coul;
+ }
+ if (vflag>0) {
+ virial[0] += delx*delx*force;
+ virial[1] += dely*dely*force;
+ virial[2] += delz*delz*force;
+ virial[3] += delx*dely*force;
+ virial[4] += delx*delz*force;
+ virial[5] += dely*delz*force;
+ }
+ }
+
+ } // for nbor
+ store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag,
+ vflag,ans,engv);
+ } // if ii
+}
+
+__kernel void k_coul_debye_fast(const __global numtyp4 *restrict x_,
+ const __global numtyp *restrict scale_in,
+ const __global numtyp *restrict sp_cl_in,
+ const __global int *dev_nbor,
+ const __global int *dev_packed,
+ __global acctyp4 *restrict ans,
+ __global acctyp *restrict engv,
+ const int eflag, const int vflag, const int inum,
+ const int nbor_pitch,
+ const __global numtyp *restrict q_,
+ const __global numtyp *restrict _cutsq,
+ const numtyp qqrd2e, const numtyp kappa,
+ const int t_per_atom) {
+ int tid, ii, offset;
+ atom_info(t_per_atom,ii,tid,offset);
+
+ __local numtyp scale[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
+ __local numtyp cutsq[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
+ __local numtyp sp_cl[4];
+ if (tid<4)
+ sp_cl[tid]=sp_cl_in[tid];
+ if (tid0) {
+ e_coul+=qqrd2e*scale[mtype]*qtmp*rinv*screening*factor_coul;
+ }
+ if (vflag>0) {
+ virial[0] += delx*delx*force;
+ virial[1] += dely*dely*force;
+ virial[2] += delz*delz*force;
+ virial[3] += delx*dely*force;
+ virial[4] += delx*delz*force;
+ virial[5] += dely*delz*force;
+ }
+ }
+
+ } // for nbor
+ store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag,
+ vflag,ans,engv);
+ } // if ii
+}
+
diff --git a/lib/gpu/lal_coul_debye.h b/lib/gpu/lal_coul_debye.h
new file mode 100644
index 0000000000..885f08cd34
--- /dev/null
+++ b/lib/gpu/lal_coul_debye.h
@@ -0,0 +1,84 @@
+/***************************************************************************
+ coul_debye.h
+ -------------------
+ Trung Dac Nguyen
+
+ Class for acceleration of the coul/debye pair style.
+
+ __________________________________________________________________________
+ This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+ __________________________________________________________________________
+
+ begin :
+ email : ndtrung@umich.edu
+ ***************************************************************************/
+
+#ifndef LAL_COUL_DEBYE_H
+#define LAL_COUL_DEBYE_H
+
+#include "lal_base_charge.h"
+
+namespace LAMMPS_AL {
+
+template
+class CoulDebye : public BaseCharge {
+ public:
+ CoulDebye();
+ ~CoulDebye();
+
+ /// Clear any previous data and set up for a new LAMMPS run
+ /** \param max_nbors initial number of rows in the neighbor matrix
+ * \param cell_size cutoff + skin
+ * \param gpu_split fraction of particles handled by device
+ *
+ * Returns:
+ * - 0 if successfull
+ * - -1 if fix gpu not found
+ * - -3 if there is an out of memory error
+ * - -4 if the GPU library was not compiled for GPU
+ * - -5 Double precision is not supported on card **/
+ int init(const int ntypes, double **host_scale,
+ double **host_cutsq, double *host_special_coul,
+ const int nlocal, const int nall, const int max_nbors,
+ const int maxspecial, const double cell_size,
+ const double gpu_split, FILE *screen,
+ const double qqrd2e, const double kappa);
+
+ /// Send updated coeffs from host to device (to be compatible with fix adapt)
+ void reinit(const int ntypes, double **host_scale);
+
+ /// Clear all host and device data
+ /** \note This is called at the beginning of the init() routine **/
+ void clear();
+
+ /// Returns memory usage on device per atom
+ int bytes_per_atom(const int max_nbors) const;
+
+ /// Total host memory used by library for pair style
+ double host_memory_usage() const;
+
+ // --------------------------- TYPE DATA --------------------------
+
+ /// scale
+ UCL_D_Vec scale;
+ /// cutsq
+ UCL_D_Vec cutsq;
+ /// Special Coul values [0-3]
+ UCL_D_Vec sp_cl;
+
+ /// If atom type constants fit in shared memory, use fast kernels
+ bool shared_types;
+
+ /// Number of atom types
+ int _lj_types;
+
+ numtyp _qqrd2e,_kappa;
+
+ private:
+ bool _allocated;
+ void loop(const bool _eflag, const bool _vflag);
+};
+
+}
+
+#endif
diff --git a/lib/gpu/lal_coul_debye_ext.cpp b/lib/gpu/lal_coul_debye_ext.cpp
new file mode 100644
index 0000000000..ced08b63e4
--- /dev/null
+++ b/lib/gpu/lal_coul_debye_ext.cpp
@@ -0,0 +1,143 @@
+/***************************************************************************
+ coul_debye_ext.cpp
+ -------------------
+ Trung Dac Nguyen
+
+ Functions for LAMMPS access to coul/debye acceleration routines.
+
+ __________________________________________________________________________
+ This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+ __________________________________________________________________________
+
+ begin :
+ email : ndtrung@umich.edu
+ ***************************************************************************/
+
+#include
+#include
+#include
+
+#include "lal_coul_debye.h"
+
+using namespace std;
+using namespace LAMMPS_AL;
+
+static CoulDebye CDEMF;
+
+// ---------------------------------------------------------------------------
+// Allocate memory on host and device and copy constants to device
+// ---------------------------------------------------------------------------
+int cdebye_gpu_init(const int ntypes, double **host_scale, double **cutsq,
+ double *host_special_coul, const int inum,
+ const int nall, const int max_nbors, const int maxspecial,
+ const double cell_size, int &gpu_mode, FILE *screen,
+ const double qqrd2e, const double kappa) {
+ CDEMF.clear();
+ gpu_mode=CDEMF.device->gpu_mode();
+ double gpu_split=CDEMF.device->particle_split();
+ int first_gpu=CDEMF.device->first_device();
+ int last_gpu=CDEMF.device->last_device();
+ int world_me=CDEMF.device->world_me();
+ int gpu_rank=CDEMF.device->gpu_rank();
+ int procs_per_gpu=CDEMF.device->procs_per_gpu();
+
+ CDEMF.device->init_message(screen,"coul/debye",first_gpu,last_gpu);
+
+ bool message=false;
+ if (CDEMF.device->replica_me()==0 && screen)
+ message=true;
+
+ if (message) {
+ fprintf(screen,"Initializing GPU and compiling on process 0...");
+ fflush(screen);
+ }
+
+ int init_ok=0;
+ if (world_me==0)
+ init_ok=CDEMF.init(ntypes, host_scale, cutsq, host_special_coul, inum, nall, 300,
+ maxspecial, cell_size, gpu_split, screen, qqrd2e, kappa);
+
+ CDEMF.device->world_barrier();
+ if (message)
+ fprintf(screen,"Done.\n");
+
+ for (int i=0; igpu_barrier();
+ if (message)
+ fprintf(screen,"Done.\n");
+ }
+ if (message)
+ fprintf(screen,"\n");
+
+ if (init_ok==0)
+ CDEMF.estimate_gpu_overhead();
+ return init_ok;
+}
+
+// ---------------------------------------------------------------------------
+// Copy updated constants to device
+// ---------------------------------------------------------------------------
+void cdebye_gpu_reinit(const int ntypes, double **host_scale) {
+ int world_me=CDEMF.device->world_me();
+ int gpu_rank=CDEMF.device->gpu_rank();
+ int procs_per_gpu=CDEMF.device->procs_per_gpu();
+
+ if (world_me==0)
+ CDEMF.reinit(ntypes, host_scale);
+
+ CDEMF.device->world_barrier();
+
+ for (int i=0; igpu_barrier();
+ }
+}
+
+void cdebye_gpu_clear() {
+ CDEMF.clear();
+}
+
+int** cdebye_gpu_compute_n(const int ago, const int inum_full,
+ const int nall, double **host_x, int *host_type,
+ double *sublo, double *subhi, tagint *tag, int **nspecial,
+ tagint **special, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ int **ilist, int **jnum, const double cpu_time,
+ bool &success, double *host_q, double *boxlo,
+ double *prd) {
+ return CDEMF.compute(ago, inum_full, nall, host_x, host_type, sublo,
+ subhi, tag, nspecial, special, eflag, vflag, eatom,
+ vatom, host_start, ilist, jnum, cpu_time, success,
+ host_q, boxlo, prd);
+}
+
+void cdebye_gpu_compute(const int ago, const int inum_full, const int nall,
+ double **host_x, int *host_type, int *ilist, int *numj,
+ int **firstneigh, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ const double cpu_time, bool &success, double *host_q,
+ const int nlocal, double *boxlo, double *prd) {
+ CDEMF.compute(ago,inum_full,nall,host_x,host_type,ilist,numj,firstneigh,eflag,
+ vflag,eatom,vatom,host_start,cpu_time,success,host_q,
+ nlocal,boxlo,prd);
+}
+
+double cdebye_gpu_bytes() {
+ return CDEMF.host_memory_usage();
+}
+
+
diff --git a/lib/gpu/lal_coul_ext.cpp b/lib/gpu/lal_coul_ext.cpp
new file mode 100644
index 0000000000..291546d5b1
--- /dev/null
+++ b/lib/gpu/lal_coul_ext.cpp
@@ -0,0 +1,143 @@
+/***************************************************************************
+ coul_ext.cpp
+ -------------------
+ Trung Dac Nguyen
+
+ Functions for LAMMPS access to coul/cut acceleration routines.
+
+ __________________________________________________________________________
+ This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+ __________________________________________________________________________
+
+ begin :
+ email : ndtrung@umich.edu
+ ***************************************************************************/
+
+#include
+#include
+#include
+
+#include "lal_coul.h"
+
+using namespace std;
+using namespace LAMMPS_AL;
+
+static Coul COULMF;
+
+// ---------------------------------------------------------------------------
+// Allocate memory on host and device and copy constants to device
+// ---------------------------------------------------------------------------
+int coul_gpu_init(const int ntypes, double **host_scale,
+ double **cutsq, double *special_coul,
+ const int inum, const int nall, const int max_nbors,
+ const int maxspecial, const double cell_size,
+ int &gpu_mode, FILE *screen, const double qqrd2e) {
+ COULMF.clear();
+ gpu_mode=COULMF.device->gpu_mode();
+ double gpu_split=COULMF.device->particle_split();
+ int first_gpu=COULMF.device->first_device();
+ int last_gpu=COULMF.device->last_device();
+ int world_me=COULMF.device->world_me();
+ int gpu_rank=COULMF.device->gpu_rank();
+ int procs_per_gpu=COULMF.device->procs_per_gpu();
+
+ COULMF.device->init_message(screen,"coul/cut",first_gpu,last_gpu);
+
+ bool message=false;
+ if (COULMF.device->replica_me()==0 && screen)
+ message=true;
+
+ if (message) {
+ fprintf(screen,"Initializing GPU and compiling on process 0...");
+ fflush(screen);
+ }
+
+ int init_ok=0;
+ if (world_me==0)
+ init_ok=COULMF.init(ntypes, host_scale, cutsq, special_coul, inum, nall, 300,
+ maxspecial, cell_size, gpu_split, screen, qqrd2e);
+
+ COULMF.device->world_barrier();
+ if (message)
+ fprintf(screen,"Done.\n");
+
+ for (int i=0; igpu_barrier();
+ if (message)
+ fprintf(screen,"Done.\n");
+ }
+ if (message)
+ fprintf(screen,"\n");
+
+ if (init_ok==0)
+ COULMF.estimate_gpu_overhead();
+ return init_ok;
+}
+
+// ---------------------------------------------------------------------------
+// Copy updated constants to device
+// ---------------------------------------------------------------------------
+void coul_gpu_reinit(const int ntypes, double **host_scale) {
+ int world_me=COULMF.device->world_me();
+ int gpu_rank=COULMF.device->gpu_rank();
+ int procs_per_gpu=COULMF.device->procs_per_gpu();
+
+ if (world_me==0)
+ COULMF.reinit(ntypes, host_scale);
+
+ COULMF.device->world_barrier();
+
+ for (int i=0; igpu_barrier();
+ }
+}
+
+void coul_gpu_clear() {
+ COULMF.clear();
+}
+
+int** coul_gpu_compute_n(const int ago, const int inum_full,
+ const int nall, double **host_x, int *host_type,
+ double *sublo, double *subhi, tagint *tag, int **nspecial,
+ tagint **special, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ int **ilist, int **jnum, const double cpu_time,
+ bool &success, double *host_q, double *boxlo,
+ double *prd) {
+ return COULMF.compute(ago, inum_full, nall, host_x, host_type, sublo,
+ subhi, tag, nspecial, special, eflag, vflag, eatom,
+ vatom, host_start, ilist, jnum, cpu_time, success,
+ host_q, boxlo, prd);
+}
+
+void coul_gpu_compute(const int ago, const int inum_full, const int nall,
+ double **host_x, int *host_type, int *ilist, int *numj,
+ int **firstneigh, const bool eflag, const bool vflag,
+ const bool eatom, const bool vatom, int &host_start,
+ const double cpu_time, bool &success, double *host_q,
+ const int nlocal, double *boxlo, double *prd) {
+ COULMF.compute(ago,inum_full,nall,host_x,host_type,ilist,numj,firstneigh,eflag,
+ vflag,eatom,vatom,host_start,cpu_time,success,host_q,
+ nlocal,boxlo,prd);
+}
+
+double coul_gpu_bytes() {
+ return COULMF.host_memory_usage();
+}
+
+
From a4edae13aedac1a7f8c2f8519480bcde5c6b9d9f Mon Sep 17 00:00:00 2001
From: sjplimp
Date: Thu, 3 Jul 2014 13:15:37 +0000
Subject: [PATCH 03/19] git-svn-id:
svn://svn.icms.temple.edu/lammps-ro/trunk@12170
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
doc/units.html | 2 +-
doc/units.txt | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/doc/units.html b/doc/units.html
index 56a06790a8..d0cff8eac7 100644
--- a/doc/units.html
+++ b/doc/units.html
@@ -61,7 +61,7 @@ results from a unitless LJ simulation into physical quantities.
Note that for LJ units, the default mode of thermodyamic output via
the thermo_style command is to normalize energies
by the number of atoms, i.e. energy/atom. This can be changed via the
-thermo_modify norm command.
+thermo_modify norm command.
For style real, these are the units:
diff --git a/doc/units.txt b/doc/units.txt
index 199d66ea26..3865ecfa70 100644
--- a/doc/units.txt
+++ b/doc/units.txt
@@ -58,7 +58,7 @@ density = mass/volume, where rho* = rho sigma^dim :ul
Note that for LJ units, the default mode of thermodyamic output via
the "thermo_style"_thermo_style.html command is to normalize energies
by the number of atoms, i.e. energy/atom. This can be changed via the
-"thermo_modify norm"_therm_modify.html command.
+"thermo_modify norm"_thermo_modify.html command.
For style {real}, these are the units:
From ff01a109a186383459f2c87c7a76cffdbc89fced Mon Sep 17 00:00:00 2001
From: sjplimp
Date: Thu, 3 Jul 2014 13:18:49 +0000
Subject: [PATCH 04/19] git-svn-id:
svn://svn.icms.temple.edu/lammps-ro/trunk@12171
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/SHOCK/fix_wall_piston.cpp | 22 +++++++---------------
1 file changed, 7 insertions(+), 15 deletions(-)
diff --git a/src/SHOCK/fix_wall_piston.cpp b/src/SHOCK/fix_wall_piston.cpp
index 8ea5a18af6..25c3b6dd3c 100644
--- a/src/SHOCK/fix_wall_piston.cpp
+++ b/src/SHOCK/fix_wall_piston.cpp
@@ -50,7 +50,7 @@ FixWallPiston::FixWallPiston(LAMMPS *lmp, int narg, char **arg) :
rampNL3flag = 0;
rampNL4flag = 0;
rampNL5flag = 0;
- x0 = y0 = z0 = vx = vy = vz = 0.0;
+ z0 = vz = 0.0;
xloflag = xhiflag = yloflag = yhiflag = zloflag = zhiflag = 0;
int iarg = 3;
@@ -71,17 +71,13 @@ FixWallPiston::FixWallPiston(LAMMPS *lmp, int narg, char **arg) :
else if (strcmp(arg[iarg],"zhi") == 0)
error->all(FLERR,"Fix wall/piston command only available at zlo");
else if (strcmp(arg[iarg],"vel") == 0) {
- if (iarg+4 > narg) error->all(FLERR,"Illegal fix wall/piston command");
- vx = force->numeric(FLERR,arg[iarg+1]);
- vy = force->numeric(FLERR,arg[iarg+2]);
- vz = force->numeric(FLERR,arg[iarg+3]);
- iarg += 4;
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix wall/piston command");
+ vz = force->numeric(FLERR,arg[iarg+1]);
+ iarg += 2;
} else if (strcmp(arg[iarg],"pos") == 0) {
- if (iarg+4 > narg) error->all(FLERR,"Illegal fix wall/piston command");
- x0 = force->numeric(FLERR,arg[iarg+1]);
- y0 = force->numeric(FLERR,arg[iarg+2]);
- z0 = force->numeric(FLERR,arg[iarg+3]);
- iarg += 4;
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix wall/piston command");
+ z0 = force->numeric(FLERR,arg[iarg+1]);
+ iarg += 2;
} else if (strcmp(arg[iarg],"temp") == 0) {
if (iarg+5 > narg) error->all(FLERR,"Illegal fix wall/piston command");
tempflag = 1;
@@ -147,11 +143,7 @@ FixWallPiston::FixWallPiston(LAMMPS *lmp, int narg, char **arg) :
}
else xscale = yscale = zscale = 1.0;
- vx *= xscale;
- vy *= yscale;
vz *= zscale;
- x0 *= xscale;
- y0 *= yscale;
z0 *= zscale;
roughdist *= zscale;
From 5490ec615ddbfef012e096b91348b64dfc6f684d Mon Sep 17 00:00:00 2001
From: sjplimp
Date: Mon, 7 Jul 2014 19:19:40 +0000
Subject: [PATCH 05/19] git-svn-id:
svn://svn.icms.temple.edu/lammps-ro/trunk@12172
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
doc/fix_wall_piston.html | 4 ++--
doc/fix_wall_piston.txt | 4 ++--
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/doc/fix_wall_piston.html b/doc/fix_wall_piston.html
index 83cc8640d7..b76361ce91 100644
--- a/doc/fix_wall_piston.html
+++ b/doc/fix_wall_piston.html
@@ -44,8 +44,8 @@
Examples:
fix xwalls all wall/piston zlo
-fix walls all wall/piston zlo pos 1.0 0.0 0.0 vel 0.0 0.0 10.0 units box
-fix top all wall/piston zlo vel 0.0 0.0 10.0 ramp
+fix walls all wall/piston zlo pos 1.0 vel 10.0 units box
+fix top all wall/piston zlo vel 10.0 ramp
Description:
diff --git a/doc/fix_wall_piston.txt b/doc/fix_wall_piston.txt
index 05bb474e86..347d1edc58 100644
--- a/doc/fix_wall_piston.txt
+++ b/doc/fix_wall_piston.txt
@@ -35,8 +35,8 @@ keyword = {pos} or {vel} or {ramp} or {units} :l
[Examples:]
fix xwalls all wall/piston zlo
-fix walls all wall/piston zlo pos 1.0 0.0 0.0 vel 0.0 0.0 10.0 units box
-fix top all wall/piston zlo vel 0.0 0.0 10.0 ramp :pre
+fix walls all wall/piston zlo pos 1.0 vel 10.0 units box
+fix top all wall/piston zlo vel 10.0 ramp :pre
[Description:]
From 3b9563910ef8e34f00c0114fbebab73136a1ae36 Mon Sep 17 00:00:00 2001
From: sjplimp
Date: Mon, 7 Jul 2014 19:19:55 +0000
Subject: [PATCH 06/19] git-svn-id:
svn://svn.icms.temple.edu/lammps-ro/trunk@12173
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
python/README | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/python/README b/python/README
index 955909f3f5..c5f7511260 100644
--- a/python/README
+++ b/python/README
@@ -34,7 +34,7 @@ scripts in the examples sub-directory:
trivial.py read/run a LAMMPS input script thru Python
demo.py invoke various LAMMPS library interface routines
-simple.py mimic operation of couple/simple/simple.cpp in Python
+simple.py mimic operation of examples/COUPLE/simple/simple.cpp
mc.py Monte Carlo energy relaxation wrapper on LAMMPS
gui.py GUI go/stop/temperature-slider to control LAMMPS
plot.py real-time temeperature plot with GnuPlot via Pizza.py
From b69c0f4ac5c3040fa42a1290c75ea1e6289ecb8b Mon Sep 17 00:00:00 2001
From: sjplimp
Date: Wed, 9 Jul 2014 17:42:16 +0000
Subject: [PATCH 07/19] git-svn-id:
svn://svn.icms.temple.edu/lammps-ro/trunk@12174
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/fix_gravity.cpp | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/src/fix_gravity.cpp b/src/fix_gravity.cpp
index 37e605f74d..24bc7b4b3c 100644
--- a/src/fix_gravity.cpp
+++ b/src/fix_gravity.cpp
@@ -248,12 +248,12 @@ void FixGravity::post_force(int vflag)
if (varflag != CONSTANT) {
modify->clearstep_compute();
if (mstyle == EQUAL) magnitude = input->variable->compute_equal(mvar);
- if (vstyle == EQUAL) magnitude = input->variable->compute_equal(vvar);
- if (pstyle == EQUAL) magnitude = input->variable->compute_equal(pvar);
- if (tstyle == EQUAL) magnitude = input->variable->compute_equal(tvar);
- if (xstyle == EQUAL) magnitude = input->variable->compute_equal(xvar);
- if (ystyle == EQUAL) magnitude = input->variable->compute_equal(yvar);
- if (zstyle == EQUAL) magnitude = input->variable->compute_equal(zvar);
+ if (vstyle == EQUAL) vert = input->variable->compute_equal(vvar);
+ if (pstyle == EQUAL) phi = input->variable->compute_equal(pvar);
+ if (tstyle == EQUAL) theta = input->variable->compute_equal(tvar);
+ if (xstyle == EQUAL) xdir = input->variable->compute_equal(xvar);
+ if (ystyle == EQUAL) ydir = input->variable->compute_equal(yvar);
+ if (zstyle == EQUAL) zdir = input->variable->compute_equal(zvar);
modify->addstep_compute(update->ntimestep + 1);
set_acceleration();
From 33186b6ad4e223e536919030135b758c8579306f Mon Sep 17 00:00:00 2001
From: pscrozi
Date: Thu, 10 Jul 2014 17:25:44 +0000
Subject: [PATCH 08/19] git-svn-id:
svn://svn.icms.temple.edu/lammps-ro/trunk@12176
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/MC/fix_gcmc.cpp | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp
index 7ecc60a682..3522653f9f 100644
--- a/src/MC/fix_gcmc.cpp
+++ b/src/MC/fix_gcmc.cpp
@@ -912,7 +912,6 @@ void FixGCMC::attempt_molecule_insertion()
for (int i = 0; i < atom->nlocal; i++) maxtag = MAX(maxtag,atom->tag[i]);
tagint maxtag_all;
MPI_Allreduce(&maxtag,&maxtag_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
- maxtag_all++;
int nfix = modify->nfix;
Fix **fix = modify->fix;
@@ -927,9 +926,9 @@ void FixGCMC::attempt_molecule_insertion()
atom->image[m] = imagetmp;
domain->remap(atom->x[m],atom->image[m]);
atom->molecule[m] = maxmol_all;
- if (maxtag_all+i >= MAXTAGINT)
+ if (maxtag_all+i+1 >= MAXTAGINT)
error->all(FLERR,"Fix gcmc ran out of available atom IDs");
- atom->tag[m] = maxtag_all + i;
+ atom->tag[m] = maxtag_all + i + 1;
atom->v[m][0] = random_unequal->gaussian()*sigma;
atom->v[m][1] = random_unequal->gaussian()*sigma;
atom->v[m][2] = random_unequal->gaussian()*sigma;
From 7e875a1ef35575d6d5b8191f147b9affa9904d3c Mon Sep 17 00:00:00 2001
From: pscrozi
Date: Thu, 10 Jul 2014 19:38:32 +0000
Subject: [PATCH 09/19] git-svn-id:
svn://svn.icms.temple.edu/lammps-ro/trunk@12177
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/MC/fix_gcmc.cpp | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp
index 3522653f9f..1d693793c6 100644
--- a/src/MC/fix_gcmc.cpp
+++ b/src/MC/fix_gcmc.cpp
@@ -937,7 +937,7 @@ void FixGCMC::attempt_molecule_insertion()
for (int j = 0; j < nfix; j++)
if (fix[j]->create_attribute) fix[j]->set_arrays(m);
- } else atom->nlocal--;
+ }
}
if (shakeflag)
From 0d6a8c5e678b6def739397fd1a186a4f042d372a Mon Sep 17 00:00:00 2001
From: pscrozi
Date: Thu, 10 Jul 2014 21:06:57 +0000
Subject: [PATCH 10/19] git-svn-id:
svn://svn.icms.temple.edu/lammps-ro/trunk@12178
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
doc/fix_gcmc.html | 10 +++++-----
doc/fix_gcmc.txt | 10 +++++-----
2 files changed, 10 insertions(+), 10 deletions(-)
diff --git a/doc/fix_gcmc.html b/doc/fix_gcmc.html
index 032364ecff..5800e4452e 100644
--- a/doc/fix_gcmc.html
+++ b/doc/fix_gcmc.html
@@ -21,9 +21,9 @@
N = invoke this fix every N steps
-X = number of exchanges to attempt every N steps
+X = number of exchanges to attempt (on average) every N steps
-M = number of MC displacements to attempt every N steps
+M = number of MC displacements to attempt (on average) every N steps
type = atom type to assign to inserted atoms (offset for molecule insertion)
@@ -68,9 +68,9 @@ potential, constant volume, and constant temperature) can be
performed. Specific uses include computing isotherms in microporous
materials, or computing vapor-liquid coexistence curves.
-Perform up to X exchanges of gas atoms or molecules of the given type
-between the simulation domain and the imaginary reservoir every N
-timesteps. Also perform M Monte Carlo displacements or rotations
+
Perform up to X exchanges (on average) of gas atoms or molecules of the
+given type between the simulation domain and the imaginary reservoir every N
+timesteps. Also perform M (on average) Monte Carlo displacements or rotations
(for molecules) of gas of the given type within the simulation domain.
M should typically be chosen to be approximately equal to the expected
number of gas atoms or molecules of the given type within the domain,
diff --git a/doc/fix_gcmc.txt b/doc/fix_gcmc.txt
index 59148b91a3..43b99034d1 100644
--- a/doc/fix_gcmc.txt
+++ b/doc/fix_gcmc.txt
@@ -15,8 +15,8 @@ fix ID group-ID gcmc N X M type seed T mu displace keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
gcmc = style name of this fix command :l
N = invoke this fix every N steps :l
-X = number of exchanges to attempt every N steps :l
-M = number of MC displacements to attempt every N steps :l
+X = number of exchanges to attempt (on average) every N steps :l
+M = number of MC displacements to attempt (on average) every N steps :l
type = atom type to assign to inserted atoms (offset for molecule insertion) :l
seed = random # seed (positive integer) :l
T = temperature of the ideal gas reservoir (temperature units) :l
@@ -52,9 +52,9 @@ potential, constant volume, and constant temperature) can be
performed. Specific uses include computing isotherms in microporous
materials, or computing vapor-liquid coexistence curves.
-Perform up to X exchanges of gas atoms or molecules of the given type
-between the simulation domain and the imaginary reservoir every N
-timesteps. Also perform M Monte Carlo displacements or rotations
+Perform up to X exchanges (on average) of gas atoms or molecules of the
+given type between the simulation domain and the imaginary reservoir every N
+timesteps. Also perform M (on average) Monte Carlo displacements or rotations
(for molecules) of gas of the given type within the simulation domain.
M should typically be chosen to be approximately equal to the expected
number of gas atoms or molecules of the given type within the domain,
From f89510ab8816521777a7ac4c8e61a83ce90a7294 Mon Sep 17 00:00:00 2001
From: pscrozi
Date: Thu, 10 Jul 2014 22:16:47 +0000
Subject: [PATCH 11/19] git-svn-id:
svn://svn.icms.temple.edu/lammps-ro/trunk@12179
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/molecule.cpp | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/molecule.cpp b/src/molecule.cpp
index 5258eb7ad4..83842af69c 100644
--- a/src/molecule.cpp
+++ b/src/molecule.cpp
@@ -151,7 +151,7 @@ void Molecule::compute_com()
com[0] = com[1] = com[2] = 0.0;
for (int i = 0; i < natoms; i++) {
if (rmassflag) onemass = rmass[i];
- else onemass = atom->type[type[i]];
+ else onemass = atom->mass[type[i]];
com[0] += x[i][0]*onemass;
com[1] += x[i][1]*onemass;
com[2] += x[i][2]*onemass;
From d1d077924fea9d8f6b546db0f104eb5fa26c269b Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer
Date: Fri, 11 Jul 2014 14:03:36 -0400
Subject: [PATCH 12/19] replace non-ASCII characters with non-accented versions
---
doc/Section_packages.txt | 2 +-
doc/Section_tools.txt | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/doc/Section_packages.txt b/doc/Section_packages.txt
index 7ede067fd8..b5bd2e81c6 100644
--- a/doc/Section_packages.txt
+++ b/doc/Section_packages.txt
@@ -370,7 +370,7 @@ See these doc pages and their related commands to get started:
"compute fep"_compute_fep.html
"soft pair styles"_pair_lj_soft.html :ul
-The person who created this package is Agilio Padua at Université
+The person who created this package is Agilio Padua at Universite
Blaise Pascal Clermont-Ferrand (agilio.padua at univ-bpclermont.fr)
Contact him directly if you have questions.
diff --git a/doc/Section_tools.txt b/doc/Section_tools.txt
index 069740824e..9bb7ba400c 100644
--- a/doc/Section_tools.txt
+++ b/doc/Section_tools.txt
@@ -239,7 +239,7 @@ The tools/fep directory contains Python scripts useful for
post-processing results from performing free-energy perturbation
simulations using the USER-FEP package.
-The scripts were contributed by Agilio Padua (Université Blaise
+The scripts were contributed by Agilio Padua (Universite Blaise
Pascal Clermont-Ferrand), agilio.padua at univ-bpclermont.fr.
See README file in the tools/fep directory.
From 97bbff4614c53cc18e276321eefec26deaeb74a6 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer
Date: Fri, 11 Jul 2014 14:04:14 -0400
Subject: [PATCH 13/19] update htmldoc input for change in communication
commands
---
lammps.book | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/lammps.book b/lammps.book
index c298c1dc6e..6045a32891 100644
--- a/lammps.book
+++ b/lammps.book
@@ -20,7 +20,8 @@ doc/box.html
doc/boundary.html
doc/change_box.html
doc/clear.html
-doc/communicate.html
+doc/comm_style.html
+doc/comm_modify.html
doc/create_atoms.html
doc/create_box.html
doc/delete_atoms.html
From 94007ab875ae957014333cac73bce4e90affb4fb Mon Sep 17 00:00:00 2001
From: sjplimp
Date: Fri, 11 Jul 2014 22:06:44 +0000
Subject: [PATCH 14/19] git-svn-id:
svn://svn.icms.temple.edu/lammps-ro/trunk@12180
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
doc/Section_modify.html | 12 +++++++++++-
doc/Section_modify.txt | 12 +++++++++++-
2 files changed, 22 insertions(+), 2 deletions(-)
diff --git a/doc/Section_modify.html b/doc/Section_modify.html
index b1d76f2898..1f1a236886 100644
--- a/doc/Section_modify.html
+++ b/doc/Section_modify.html
@@ -650,7 +650,7 @@ directory.
Note that by providing us the files to release, you are agreeing to
make them open-source, i.e. we can release them under the terms of the
-GPL used as a license for the rest of LAMMPS. See Section
+GPL, used as a license for the rest of LAMMPS. See Section
1.4 for details.
With user packages and files, all we are really providing (aside from
@@ -664,6 +664,16 @@ agreeing to support your code which means answer questions, fix bugs,
and maintain it if LAMMPS changes in some way that breaks it (an
unusual event).
+NOTE: If you prefer to actively develop and support your add-on
+feature yourself, then you may wish to make it available for download
+from your own website, as a user package that LAMMPS users can add to
+their copy of LAMMPS. See the Offsite LAMMPS packages and
+tools page of the LAMMPS web
+site for examples of groups that do this. We are happy to advertise
+your package and web site from that page. Simply email the
+developers with info about
+your package and we will post it there.
+
The previous sections of this doc page describe how to add new "style"
files of various kinds to LAMMPS. Packages are simply collections of
one or more new class files which are invoked as a new style within a
diff --git a/doc/Section_modify.txt b/doc/Section_modify.txt
index 109892e1ee..a5068f80fe 100644
--- a/doc/Section_modify.txt
+++ b/doc/Section_modify.txt
@@ -624,7 +624,7 @@ directory.
Note that by providing us the files to release, you are agreeing to
make them open-source, i.e. we can release them under the terms of the
-GPL used as a license for the rest of LAMMPS. See "Section
+GPL, used as a license for the rest of LAMMPS. See "Section
1.4"_Section_intro.html#intro_4 for details.
With user packages and files, all we are really providing (aside from
@@ -638,6 +638,16 @@ agreeing to support your code which means answer questions, fix bugs,
and maintain it if LAMMPS changes in some way that breaks it (an
unusual event).
+NOTE: If you prefer to actively develop and support your add-on
+feature yourself, then you may wish to make it available for download
+from your own website, as a user package that LAMMPS users can add to
+their copy of LAMMPS. See the "Offsite LAMMPS packages and
+tools"_http://lammps.sandia.gov/offsite.html page of the LAMMPS web
+site for examples of groups that do this. We are happy to advertise
+your package and web site from that page. Simply email the
+"developers"_http://lammps.sandia.gov/authors.html with info about
+your package and we will post it there.
+
The previous sections of this doc page describe how to add new "style"
files of various kinds to LAMMPS. Packages are simply collections of
one or more new class files which are invoked as a new style within a
From 0d4c0446b79f80f472b88abac3c34d8a8646e6ed Mon Sep 17 00:00:00 2001
From: sjplimp
Date: Fri, 11 Jul 2014 22:10:48 +0000
Subject: [PATCH 15/19] git-svn-id:
svn://svn.icms.temple.edu/lammps-ro/trunk@12181
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
potentials/CuNi.eam.alloy | 708 ++++++++++++++++++++++++++++++++++++++
1 file changed, 708 insertions(+)
create mode 100644 potentials/CuNi.eam.alloy
diff --git a/potentials/CuNi.eam.alloy b/potentials/CuNi.eam.alloy
new file mode 100644
index 0000000000..8185d77a97
--- /dev/null
+++ b/potentials/CuNi.eam.alloy
@@ -0,0 +1,708 @@
+Cu-Ni EAM potential (DYNAMO setfl format)
+Berk Onat, Sondan Durukanoglu, J. Phys.:Condens. Matter, 26 (2014) 035404
+onat@seas.harvard.edu, sondan@sabanciuniv.edu
+ 2 Ni Cu
+ 500 0.5957203073046090E-02 500 0.1281429334268537E-01 0.6394332378000000E+01
+ 28 58.689 3.5200 FCC
+ 0.0000000000000000E+00 0.2310449218913587E+00 0.3601934353256622E+00 0.4621124611164747E+00 0.5503537468978359E+00
+ 0.6300757963542245E+00 0.7038802455938034E+00 0.7732905416725754E+00 0.8392257089968028E+00 0.9027865328157253E+00
+ 0.9658194860639715E+00 0.1027826247879761E+01 0.1088832782192100E+01 0.1148894077704396E+01 0.1208076079524810E+01
+ 0.1266446899313574E+01 0.1324072597342345E+01 0.1381015276264052E+01 0.1437332357564334E+01 0.1493076463074613E+01
+ 0.1548295594820588E+01 0.1603033452584359E+01 0.1657329803809591E+01 0.1711220857122843E+01 0.1764739622611741E+01
+ 0.1817916241550007E+01 0.1870778288872414E+01 0.1923351040637830E+01 0.1975657715472759E+01 0.2027719686701964E+01
+ 0.2079556671143745E+01 0.2131186894592996E+01 0.2182627240308380E+01 0.2233893378931416E+01 0.2284999884106182E+01
+ 0.2335960335573459E+01 0.2386787409459689E+01 0.2437492960973464E+01 0.2488088043214997E+01 0.2538581543968955E+01
+ 0.2588955467236866E+01 0.2638445004384797E+01 0.2688553901592873E+01 0.2739945095110078E+01 0.2791985258776929E+01
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+ -0.1700805999031528E-01 -0.1551728323748941E-01 -0.1408596049940787E-01 -0.1271516917577567E-01 -0.1140604336513917E-01
+ -0.1015977609190218E-01 -0.8977620986254353E-02 -0.7860894474044497E-02 -0.6810977925945496E-02 -0.5829319881680835E-02
+ -0.4917438351640220E-02 -0.4076923198389168E-02 -0.3309438600477362E-02 -0.2616725601205811E-02 -0.2000604744978047E-02
+ -0.1462978803952002E-02 -0.1005835597839964E-02 -0.6312509097629686E-03 -0.3413915010994390E-03 -0.1385182284627833E-03
+ -0.2499288957546912E-04 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00
+ 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00 0.0000000000000000E+00
+
From 331fe9b10bff4f217043528f401524e39a9f943c Mon Sep 17 00:00:00 2001
From: sjplimp
Date: Fri, 11 Jul 2014 22:12:45 +0000
Subject: [PATCH 16/19] git-svn-id:
svn://svn.icms.temple.edu/lammps-ro/trunk@12182
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/version.h | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/version.h b/src/version.h
index 8e7a4ef385..7e1adf092b 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "28 Jun 2014"
+#define LAMMPS_VERSION "11 Jul 2014"
From 164832591d0d8822a419f8b1b87281a5b99aa31d Mon Sep 17 00:00:00 2001
From: sjplimp
Date: Fri, 11 Jul 2014 22:12:46 +0000
Subject: [PATCH 17/19] git-svn-id:
svn://svn.icms.temple.edu/lammps-ro/trunk@12183
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
doc/Manual.html | 4 ++--
doc/Manual.txt | 4 ++--
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/doc/Manual.html b/doc/Manual.html
index fa751a5b09..41c9884fe9 100644
--- a/doc/Manual.html
+++ b/doc/Manual.html
@@ -1,7 +1,7 @@
LAMMPS Users Manual
-
+
@@ -22,7 +22,7 @@
LAMMPS Documentation
-28 Jun 2014 version
+11 Jul 2014 version
Version info:
diff --git a/doc/Manual.txt b/doc/Manual.txt
index bbff8a94a9..6e5c3a3c00 100644
--- a/doc/Manual.txt
+++ b/doc/Manual.txt
@@ -1,6 +1,6 @@
LAMMPS Users Manual
-
+
@@ -18,7 +18,7 @@
LAMMPS Documentation :c,h3
-28 Jun 2014 version :c,h4
+11 Jul 2014 version :c,h4
Version info: :h4
From 70a5d02c8db3ed39cfe2abbfbc63cf53880d5b6f Mon Sep 17 00:00:00 2001
From: sjplimp
Date: Mon, 14 Jul 2014 16:10:59 +0000
Subject: [PATCH 18/19] git-svn-id:
svn://svn.icms.temple.edu/lammps-ro/trunk@12185
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
doc/fix_bond_swap.html | 11 +++++------
doc/fix_bond_swap.txt | 4 ++--
2 files changed, 7 insertions(+), 8 deletions(-)
diff --git a/doc/fix_bond_swap.html b/doc/fix_bond_swap.html
index 1f4eca588c..2c38100e53 100644
--- a/doc/fix_bond_swap.html
+++ b/doc/fix_bond_swap.html
@@ -13,13 +13,12 @@
Syntax:
-fix ID group-ID bond/swap fraction cutoff seed
+fix ID group-ID bond/swap Nevery fraction cutoff seed
-
ID, group-ID are documented in fix command
-bond/swap = style name of this fix command
-Nevery = attempt bond swapping every this many steps
-
-- fraction = fraction of group atoms to consider for swapping
+
- ID, group-ID are documented in fix command
+
- bond/swap = style name of this fix command
+
- Nevery = attempt bond swapping every this many steps
+
- fraction = fraction of group atoms to consider for swapping
- cutoff = distance at which swapping will be considered (distance units)
- seed = random # seed (positive integer)
diff --git a/doc/fix_bond_swap.txt b/doc/fix_bond_swap.txt
index 1a0499957e..2e418f9151 100755
--- a/doc/fix_bond_swap.txt
+++ b/doc/fix_bond_swap.txt
@@ -10,11 +10,11 @@ fix bond/swap command :h3
[Syntax:]
-fix ID group-ID bond/swap fraction cutoff seed :pre
+fix ID group-ID bond/swap Nevery fraction cutoff seed :pre
ID, group-ID are documented in "fix"_fix.html command
bond/swap = style name of this fix command
-Nevery = attempt bond swapping every this many steps :l
+Nevery = attempt bond swapping every this many steps
fraction = fraction of group atoms to consider for swapping
cutoff = distance at which swapping will be considered (distance units)
seed = random # seed (positive integer) :ul
From b2cb1b35728afe789dca41129da515a4951b40d1 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer
Date: Mon, 21 Jul 2014 18:45:28 -0400
Subject: [PATCH 19/19] enable storing custom per atom properties in fix
store/state
---
src/fix_store_state.cpp | 49 ++++++++++++++++++++++++++++++++++++++++-
1 file changed, 48 insertions(+), 1 deletion(-)
diff --git a/src/fix_store_state.cpp b/src/fix_store_state.cpp
index e70eada845..d2ecdbcc5f 100644
--- a/src/fix_store_state.cpp
+++ b/src/fix_store_state.cpp
@@ -30,7 +30,7 @@
using namespace LAMMPS_NS;
using namespace FixConst;
-enum{KEYWORD,COMPUTE,FIX,VARIABLE};
+enum{KEYWORD,COMPUTE,FIX,VARIABLE,DNAME,INAME};
#define INVOKED_PERATOM 8
@@ -198,11 +198,15 @@ FixStoreState::FixStoreState(LAMMPS *lmp, int narg, char **arg) :
pack_choice[nvalues++] = &FixStoreState::pack_tqz;
} else if (strncmp(arg[iarg],"c_",2) == 0 ||
+ strncmp(arg[iarg],"d_",2) == 0 ||
strncmp(arg[iarg],"f_",2) == 0 ||
+ strncmp(arg[iarg],"i_",2) == 0 ||
strncmp(arg[iarg],"v_",2) == 0) {
cfv_any = 1;
if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
+ else if (arg[iarg][0] == 'd') which[nvalues] = DNAME;
else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
+ else if (arg[iarg][0] == 'i') which[nvalues] = INAME;
else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
int n = strlen(arg[iarg]);
@@ -265,6 +269,20 @@ FixStoreState::FixStoreState(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,
"Fix store/state compute array is accessed out-of-range");
+ } else if (which[i] == INAME) {
+ int icustom,iflag;
+ icustom = atom->find_custom(ids[i],iflag);
+ if ((icustom < 0) || (iflag != 0))
+ error->all(FLERR,
+ "Custom integer vector does not exist");
+
+ } else if (which[i] == DNAME) {
+ int icustom,iflag;
+ icustom = atom->find_custom(ids[i],iflag);
+ if ((icustom < 0) || (iflag != 1))
+ error->all(FLERR,
+ "Custom floating point vector does not exist");
+
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
@@ -369,6 +387,23 @@ void FixStoreState::init()
error->all(FLERR,"Compute ID for fix store/state does not exist");
value2index[m] = icompute;
+ } else if (which[m] == INAME) {
+ int icustom,iflag;
+ icustom = atom->find_custom(ids[m],iflag);
+ if ((icustom < 0) || (iflag != 0))
+ error->all(FLERR,
+ "Custom integer vector for fix store/state does not exist");
+ value2index[m] = icustom;
+
+ } else if (which[m] == DNAME) {
+ int icustom,iflag;
+ icustom = atom->find_custom(ids[m],iflag);
+ if ((icustom < 0) || (iflag != 1))
+ error->all(FLERR,
+ "Custom floating point vector for fix"
+ " store/state does not exist");
+ value2index[m] = icustom;
+
} else if (which[m] == FIX) {
int ifix = modify->find_fix(ids[m]);
if (ifix < 0)
@@ -465,6 +500,18 @@ void FixStoreState::end_of_step()
if (mask[i] & groupbit) values[i][m] = fix_array[i][jm1];
}
+ // access custom atom property fields
+
+ } else if (which[m] == INAME) {
+ int *ivector = atom->ivector[n];
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) values[i][m] = ivector[i];
+
+ } else if (which[m] == DNAME) {
+ double *dvector = atom->dvector[n];
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) values[i][m] = dvector[i];
+
// evaluate atom-style variable
} else if (which[m] == VARIABLE) {