Merge pull request #91 from GOMC-WSU/development

Hotfix - v2.31
GOMC-WSU · May 21, 2018 · 50885b8 · 50885b8
2 parents 7dcb2e3 + 0bfc8f9
commit 50885b8
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -16,7 +16,7 @@ set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
 
 #Versioning
 set (GOMC_VERSION_MAJOR 2)
-set (GOMC_VERSION_MINOR 30)
+set (GOMC_VERSION_MINOR 31)
 
 IF(NOT CMAKE_BUILD_TYPE)
    SET(CMAKE_BUILD_TYPE Release CACHE STRING

diff --git a/Change log b/Change log
@@ -1,6 +1,13 @@
 # Change Log
 All notable changes to this project will be documented in this file.
 
+## [2.31] - 5/21/2018
++ Compiling problem fixed on CYGWIN
++ Fix to the error checking of volume exchange if simulation volume became negative
++ Fix the equation to impose fix angle if the angle is less than 90. Generate error if constrained angle is not possible.
++ Fixed a bug where move timings were 0 in windows.
++ Fixed the issue where input files imported from NVT to NPT had zero volume, default value of 500 will be assigned in those cases.
+
 ## [2.30] - 5/10/2018
 + Added Regrowth move
 + Cleaned up the code and removed any memory leaks and bugs.

diff --git a/README.md b/README.md
@@ -1,45 +1,53 @@
-Current Release: 2.30 (5/1/2018)
+# GOMC - GPU Optimized Monte Carlo
+
+Current Release: 2.31 (5/21/2018)
 
 [![Gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/GOMC_WSU/Lobby?utm_source=share-link&utm_medium=link&utm_campaign=share-link)
 [![Build Status](https://travis-ci.org/GOMC-WSU/GOMC.svg?branch=master)](https://travis-ci.org/GOMC-WSU/GOMC)
 
 We recommend the [GOMC Project Website](http://gomc.eng.wayne.edu/ "GOMC Website") and the [user manual](http://gomc.eng.wayne.edu/GOMC_files/GOMC_Manual.pdf "User Manual") for further information and examples.
 
-GOMC - GPU Optimized Monte Carlo
-============
-
-BUILDING GOMC ON LINUX:
-----------------
-   1. Clone or download our code from GitHub using "git clone https://github.com/GOMC-WSU/GOMC.git"
-   2. Go into the GOMC directory using "cd GOMC"
-   3. Give execution permission using "chmod u+x metamake.sh"
-   4. In the base directory type "./metamake.sh"
-   5. Step 2 should generate all the executables in "bin" directory
-
-   You can set the number of the threads using the +pN argument, where N is the number of threads.
-   For example:
-      ./GOMC_<CPU|GPU>_XXXX +p4 in.conf
-      Which will run 4 threads and reads input file "in.conf".
-
-   NOTES:
-      Building GOMC requires cmake, available at http://www.cmake.org and
-      in most Linux package repositories (as cmake).
-      If you wish to utilize NVIDIA graphic cards you will need to install
-      NVIDIA toolkit before compiling. The metamake file will automatically
-      detect the location of CUDA installation. (More info in Manual)
-
-BUILDING GOMC ON WINDOWS:
------------------
-   1. Open the Windows-compatible CMake GUI.
-   2. Set the Source Folder to the GOMC root folder.
-   3. Set the build Folder to your Build Folder.
-   4. Click configure, select your compiler/environment
-   5. Wait for CMake to finish the configuration.
-   6. Click configure again and click generate.
-   7. Open the CMake-generated project/solution etc. to the desired IDE
-      (e.g Visual Studio).
-   8. Using the solution in the IDE of choice build GOMC per the IDE's
-      standard release compilation/executable generation methods.
+## Building GOMC on GNU/Linux, macOS, or Cygwin:
+
+  1. Clone or download our code from GitHub:
+      ```bash
+      git clone https://github.com/GOMC-WSU/GOMC.git
+      ```
+  2. Go into the GOMC directory: 
+      ```bash
+      cd GOMC
+      ```
+  3. Give execution permission: 
+      ```bash
+      chmod u+x metamake.sh
+      ```
+  4. Run metamake file:
+      ```bash
+      ./metamake.sh
+      ```
+  5. Step 4 should generate all the executables in ```bin``` directory
+
+  You can set the number of the threads using the +pN argument, where N is the number of threads.
+  For example:
+  ```bash
+  ./GOMC_<CPU|GPU>_XXXX +p4 in.conf
+  ```
+
+  Which will run 4 threads and reads input file "in.conf".
+
+  NOTES:
+  Building GOMC requires cmake, available at http://www.cmake.org and in most Linux package repositories (as cmake).
+  If you wish to utilize NVIDIA graphic cards you will need to install NVIDIA toolkit before compiling. The metamake file will automatically detect the location of CUDA installation. (More info in Manual)
+
+## BUILDING GOMC ON WINDOWS:
+  1. Open the Windows-compatible CMake GUI.
+  2. Set the Source Folder to the GOMC root folder.
+  3. Set the build Folder to your Build Folder.
+  4. Click configure, select your compiler/environment
+  5. Wait for CMake to finish the configuration.
+  6. Click configure again and click generate.
+  7. Open the CMake-generated project/solution etc. to the desired IDE (e.g Visual Studio).
+  8. Using the solution in the IDE of choice build GOMC per the IDE's standard release compilation/executable generation methods.
 
    NOTES:
       You can also use CMake from the Windows command line if its directory is

diff --git a/lib/BasicTypes.h b/lib/BasicTypes.h
@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.30
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.31
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

diff --git a/lib/BitLib.h b/lib/BitLib.h
@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.30
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.31
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

diff --git a/lib/GeomLib.h b/lib/GeomLib.h
@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.30
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.31
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

diff --git a/lib/NumLib.h b/lib/NumLib.h
@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.30
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.31
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

diff --git a/lib/StrLib.h b/lib/StrLib.h
@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.30
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.31
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

diff --git a/lib/StrStrmLib.h b/lib/StrStrmLib.h
@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.30
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.31
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

diff --git a/lib/VectorLib.h b/lib/VectorLib.h
@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.30
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.31
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

diff --git a/src/BlockOutput.cpp b/src/BlockOutput.cpp
@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.30
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.31
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

diff --git a/src/BlockOutput.h b/src/BlockOutput.h
@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.30
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.31
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

diff --git a/src/BoxDimensions.cpp b/src/BoxDimensions.cpp
@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.30
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.31
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.
@@ -18,6 +18,7 @@ void BoxDimensions::Init(config_setup::RestartSettings const& restart,
 {
   rCut = rc;
   rCutSq = rcSq;
+  minVol = 8.0 * rCutSq * rCut + 0.001;
   for (uint b = 0; b < BOX_TOTAL; b++) {
     if(restart.enable && cryst.hasVolume) {
       axis = cryst.axis;
@@ -50,17 +51,17 @@ void BoxDimensions::Init(config_setup::RestartSettings const& restart,
 
     //Print Box dimensio info
     printf("%s %-d: %-26s %6.3f %7.3f %7.3f \n",
-           "Info: Box ", b, " Periodic Cell Basis 1",
-           cellBasis[b].Get(0).x, cellBasis[b].Get(0).y,
-           cellBasis[b].Get(0).z);
+	   "Info: Box ", b, " Periodic Cell Basis 1",
+	   cellBasis[b].Get(0).x, cellBasis[b].Get(0).y,
+	   cellBasis[b].Get(0).z);
     printf("%s %-d: %-26s %6.3f %7.3f %7.3f \n",
-           "Info: Box ", b, " Periodic Cell Basis 2",
-           cellBasis[b].Get(1).x, cellBasis[b].Get(1).y,
-           cellBasis[b].Get(1).z);
+	   "Info: Box ", b, " Periodic Cell Basis 2",
+	   cellBasis[b].Get(1).x, cellBasis[b].Get(1).y,
+	   cellBasis[b].Get(1).z);
     printf("%s %-d: %-26s %6.3f %7.3f %7.3f \n\n",
-           "Info: Box ", b, " Periodic Cell Basis 3",
-           cellBasis[b].Get(2).x, cellBasis[b].Get(2).y,
-           cellBasis[b].Get(2).z);
+	   "Info: Box ", b, " Periodic Cell Basis 3",
+	   cellBasis[b].Get(2).x, cellBasis[b].Get(2).y,
+	   cellBasis[b].Get(2).z);
 
 
     axis.Set(b, cellBasis[b].Length(0), cellBasis[b].Length(1),
@@ -106,7 +107,7 @@ uint BoxDimensions::ShiftVolume
   //If move would shrink any box axis to be less than 2 * rcut, then
   //automatically reject to prevent errors.
   if ((newDim.halfAx.x[b] < rCut || newDim.halfAx.y[b] < rCut ||
-       newDim.halfAx.z[b] < rCut)) {
+       newDim.halfAx.z[b] < rCut || newVolume < minVol)) {
     std::cout << "WARNING!!! box shrunk below 2*Rcut! Auto-rejecting!"
               << std::endl;
     std::cout << "AxisDimensions: " << newDim.GetAxis(b) << std::endl;
@@ -131,7 +132,7 @@ uint BoxDimensions::ExchangeVolume
   for (uint b = 0; b < BOX_TOTAL; b++) {
     scale[b] = newDim.axis.Get(b) / axis.Get(b);
     if ((newDim.halfAx.x[b] < rCut || newDim.halfAx.y[b] < rCut ||
-         newDim.halfAx.z[b] < rCut)) {
+         newDim.halfAx.z[b] < rCut || newDim.volume[b] < minVol)) {
       std::cout << "WARNING!!! box shrunk below 2*Rcut! Auto-rejecting!"
                 << std::endl;
       std::cout << "AxisDimensions: " << newDim.GetAxis(b) << std::endl;

diff --git a/src/BoxDimensions.h b/src/BoxDimensions.h
@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.30
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.31
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.
@@ -135,6 +135,7 @@ class BoxDimensions
 
   double rCut;
   double rCutSq;
+  double minVol;
 
   bool cubic[BOX_TOTAL], orthogonal[BOX_TOTAL], constArea;
 

diff --git a/src/BoxDimensionsNonOrth.cpp b/src/BoxDimensionsNonOrth.cpp
@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.30
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.31
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.
@@ -18,6 +18,7 @@ void BoxDimensionsNonOrth::Init(config_setup::RestartSettings const& restart,
 {
   rCut = rc;
   rCutSq = rcSq;
+  minVol = 8.0 * rCutSq * rCut + 0.001;
   for (uint b = 0; b < BOX_TOTAL; b++) {
     if(restart.enable && cryst.hasVolume) {
       axis = cryst.axis;
@@ -50,17 +51,17 @@ void BoxDimensionsNonOrth::Init(config_setup::RestartSettings const& restart,
 
     //Print Box dimensio info
     printf("%s %-d: %-26s %6.3f %7.3f %7.3f \n",
-           "Info: Box ", b, " Periodic Cell Basis 1",
-           cellBasis[b].Get(0).x, cellBasis[b].Get(0).y,
-           cellBasis[b].Get(0).z);
+	   "Info: Box ", b, " Periodic Cell Basis 1",
+	   cellBasis[b].Get(0).x, cellBasis[b].Get(0).y,
+	   cellBasis[b].Get(0).z);
     printf("%s %-d: %-26s %6.3f %7.3f %7.3f \n",
-           "Info: Box ", b, " Periodic Cell Basis 2",
-           cellBasis[b].Get(1).x, cellBasis[b].Get(1).y,
-           cellBasis[b].Get(1).z);
+	   "Info: Box ", b, " Periodic Cell Basis 2",
+	   cellBasis[b].Get(1).x, cellBasis[b].Get(1).y,
+	   cellBasis[b].Get(1).z);
     printf("%s %-d: %-26s %6.3f %7.3f %7.3f \n\n",
-           "Info: Box ", b, " Periodic Cell Basis 3",
-           cellBasis[b].Get(2).x, cellBasis[b].Get(2).y,
-           cellBasis[b].Get(2).z);
+	   "Info: Box ", b, " Periodic Cell Basis 3",
+	   cellBasis[b].Get(2).x, cellBasis[b].Get(2).y,
+	   cellBasis[b].Get(2).z);
 
 
     //Find the length of a, b, c
@@ -156,7 +157,7 @@ uint BoxDimensionsNonOrth::ShiftVolume(BoxDimensionsNonOrth & newDim,
   //If move would shrink any box axis to be less than 2 * rcut, then
   //automatically reject to prevent errors.
   if ((newDim.halfAx.x[b] < rCut || newDim.halfAx.y[b] < rCut ||
-       newDim.halfAx.z[b] < rCut)) {
+       newDim.halfAx.z[b] < rCut || newVolume < minVol)) {
     std::cout << "WARNING!!! box shrunk below 2*Rcut! Auto-rejecting!"
               << std::endl;
     std::cout << "AxisDimensions: " << newDim.GetAxis(b) << std::endl;
@@ -180,14 +181,14 @@ uint BoxDimensionsNonOrth::ExchangeVolume(BoxDimensionsNonOrth & newDim,
 
   //If move would shrink any box axis to be less than 2 * rcut, then
   //automatically reject to prevent errors.
-  for (uint b = 0; b < BOX_TOTAL && state == mv::fail_state::NO_FAIL; b++) {
+  for (uint b = 0; b < BOX_TOTAL; b++) {
     scale[b] = newDim.axis.Get(b) / axis.Get(b);
     if ((newDim.halfAx.x[b] < rCut || newDim.halfAx.y[b] < rCut ||
-         newDim.halfAx.z[b] < rCut)) {
+         newDim.halfAx.z[b] < rCut || newDim.volume[b] < minVol)) {
       std::cout << "WARNING!!! box shrunk below 2*Rcut! Auto-rejecting!"
                 << std::endl;
       std::cout << "AxisDimensions: " << newDim.GetAxis(b) << std::endl;
-      state = mv::fail_state::VOL_TRANS_WOULD_SHRINK_BOX_BELOW_CUTOFF;
+      return  mv::fail_state::VOL_TRANS_WOULD_SHRINK_BOX_BELOW_CUTOFF;
     }
   }
   return state;

diff --git a/src/BoxDimensionsNonOrth.h b/src/BoxDimensionsNonOrth.h
@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.30
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.31
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

diff --git a/src/CBMC.cpp b/src/CBMC.cpp
@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.30
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.31
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

diff --git a/src/CBMC.h b/src/CBMC.h
@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.30
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.31
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

diff --git a/src/COM.h b/src/COM.h
@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.30
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.31
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

diff --git a/src/CPUSide.cpp b/src/CPUSide.cpp
@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.30
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.31
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

diff --git a/src/CPUSide.h b/src/CPUSide.h
@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.30
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.31
 Copyright (C) 2018  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.