Merge branch 'master' of https://gitlab.msu.edu/SParTA/PuReMD.

README.md

-## Introduction
+[Introduction](https://gitlab.msu.edu/SParTA/PuReMD#introduction) |
+[Documentation](https://gitlab.msu.edu/SParTA/PuReMD/doc) |
+[Wiki](https://gitlab.msu.edu/SParTA/PuReMD/wikis/home)
 
-Files from the [Purdue Reactive Molecular Dynamics](https://www.cs.purdue.edu/puremd) (PuReMD) project.
+# Introduction
 
-## Relevant Papers
+This repository contains the development version of the
+[Purdue Reactive Molecular Dynamics](https://www.cs.purdue.edu/puremd) (PuReMD) project.
 
-Roughly by target platform
+# Build Instructions
+
+## Developer
+
+To build, the following versions of software are required:
+
+- git
+- Autoconf v2.69+
+- Automake v1.15+
+- OpenMP v4.0+ compliant compiler (OpenMP versions only)
+- MPI v2+ compliant library (MPI versions only)
+- CUDA v6.0+ (CUDA versions only)
+
+Instructions:
+```bash
+	git clone https://gitlab.msu.edu/SParTA/PuReMD.git
+	cd PuReMD
+	git submodule init
+	git submodule update
+	autoreconf -ivf
+	./configure
+	make
+```
+
+To build tarball releases after configuring a specific build target, run the following:
+
+```bash
+	make dist
+```
+
+## User
+
+```bash
+	# Download release tarball
+	tar -xvf puremd-1.0.tar.gz
+	cd puremd-1.0
+	./configure
+	make
+```
+
+By default, the shared memory version with OpenMP support will be built. For other build targets,
+run ./configure --help and consult the documentation. An example of building the MPI+CUDA version
+is given below.
+
+```bash
+	./configure --enable-openmp=no --enable-mpi-gpu=yes
+```
+
+# References
+
+Shared Memory:
 - [Serial](https://www.cs.purdue.edu/puremd/docs/80859.pdf)
-- [MPI (message passing interface)](https://www.cs.purdue.edu/puremd/docs/Parallel-Reactive-Molecular-Dynamics.pdf)
 - [CUDA (single GPU)](http://dx.doi.org/10.1016/j.jcp.2014.04.035)
+- [Charge Method Optimizations with OpenMP](https://doi.org/10.1109/ScalA.2016.006)
+
+Distributed Memory:
+- [MPI (message passing interface)](https://www.cs.purdue.edu/puremd/docs/Parallel-Reactive-Molecular-Dynamics.pdf)
 - [CUDA+MPI (multi-GPU)](https://www.cs.purdue.edu/puremd/docs/pgpuremd.pdf)

sPuReMD/src/forces.c

@@ -488,11 +488,11 @@ static void Init_Charge_Matrix_Remaining_Entries( reax_system *system,
             for ( i = 0; i < system->N; ++i )
             {
                 H->j[*Htop] = i;
-                H->val[*Htop] = -1.0;
+                H->val[*Htop] = 1.0;
                 *Htop = *Htop + 1;
 
                 H_sp->j[*H_sp_top] = i;
-                H_sp->val[*H_sp_top] = -1.0;
+                H_sp->val[*H_sp_top] = 1.0;
                 *H_sp_top = *H_sp_top + 1;
             }
 
@@ -510,11 +510,11 @@ static void Init_Charge_Matrix_Remaining_Entries( reax_system *system,
                 H_sp->start[system->N + i + 1] = *H_sp_top;
 
                 H->j[*Htop] = i;
-                H->val[*Htop] = -1.0;
+                H->val[*Htop] = 1.0;
                 *Htop = *Htop + 1;
 
                 H_sp->j[*H_sp_top] = i;
-                H_sp->val[*H_sp_top] = -1.0;
+                H_sp->val[*H_sp_top] = 1.0;
                 *H_sp_top = *H_sp_top + 1;
 
                 for ( pj = Start_Index(i, far_nbrs); pj < End_Index(i, far_nbrs); ++pj )
@@ -583,11 +583,11 @@ static void Init_Charge_Matrix_Remaining_Entries( reax_system *system,
             for ( i = system->N + 1; i < system->N_cm - 1; ++i )
             {
                 H->j[*Htop] = i;
-                H->val[*Htop] = -1.0;
+                H->val[*Htop] = 1.0;
                 *Htop = *Htop + 1;
 
                 H_sp->j[*H_sp_top] = i;
-                H_sp->val[*H_sp_top] = -1.0;
+                H_sp->val[*H_sp_top] = 1.0;
                 *H_sp_top = *H_sp_top + 1;
             }