Add new random number generators

README.md

@@ -5,7 +5,7 @@ Fast, parallelized molecular dynamics trajectory data analysis.
 
 Build Status
 =============
-* Travis-CI: [![Travis Build Status](https://travis-ci.org/Amber-MD/cpptraj.svg?branch=master)](https://travis-ci.org/Amber-MD/cpptraj)
+* GitHub Actions: [![GitHub Actions Status](https://github.com/Amber-MD/cpptraj/actions/workflows/merge-gate.yml/badge.svg)](https://github.com/Amber-MD/cpptraj/actions)
 * AppVeyor: [![Windows Build Status](https://ci.appveyor.com/api/projects/status/github/Amber-MD/cpptraj?branch=master&svg=true&retina=true)](https://ci.appveyor.com/project/drroe/cpptraj-aof9y/branch/master)
 * Jenkins: [![Jenkins Build Status](https://jenkins.jasonswails.com/buildStatus/icon?job=amber-github%2Fcpptraj%2Fmaster&style=plastic)](https://jenkins.jasonswails.com/job/amber-github/job/cpptraj/job/master/)
 * LGTM: [![Language grade: C/C++](https://img.shields.io/lgtm/grade/cpp/g/Amber-MD/cpptraj.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/Amber-MD/cpptraj/context:cpp)
@@ -84,10 +84,12 @@ the following libraries:
 
 CPPTRAJ also makes use of the following libraries that are bundled with CPPTRAJ. External ones can be used in place of these if desired.
 
-* ARPACK; without this diagonalization of sparse matrices in `diagmatrix` will be slow
-* [helPME](https://github.com/andysim/helpme), required for PME functionality
-* XDR for reading GROMACS XTC trajectories
-* TNG for reading GROMACS TNG trajectories
+* ARPACK; without this diagonalization of sparse matrices in `diagmatrix` will be slow.
+* [helPME](https://github.com/andysim/helpme) by Andy Simmonett, required for PME functionality.
+* XDR for reading GROMACS XTC trajectories.
+* TNG for reading GROMACS TNG trajectories.
+
+CPPTRAJ also uses the PCG32 and Xoshiro 128++ pseudo-random number generators.
 
 `./configure gnu` should be adequate to set up compilation for most systems.
 For systems without BLAS/LAPACK/ARPACK and/or NetCDF libraries installed,
@@ -213,8 +215,8 @@ Original implementation of the Amber NetCDF trajectory format.
 * Hannes H. Loeffler (STFC Daresbury, Scientific Computing Department, Warrington, WA4 4AD, UK)
 Diffusion calculation code adapted for use in Action\_STFC\_Diffusion.
 
-External libraries bundled with CPPTRAJ
-=======================================
+External code/libraries bundled with CPPTRAJ
+============================================
 
 * CPPTRAJ makes use of the [GNU readline](https://tiswww.case.edu/php/chet/readline/rltop.html) library for the interactive command line.
 
@@ -227,3 +229,5 @@ External libraries bundled with CPPTRAJ
 * The reciprocal part of the PME calculation is handled by the [helPME](https://github.com/andysim/helpme) library by Andy Simmonett.
 
 * Support for reading DTR trajectories uses the VMD DTR plugin.
+
+* CPPTRAJ uses code for the [permuted congruent pseudo-random number generator](https://www.pcg-random.org/index.html) PCG32 by Melissa O'Neill and the [Xoshiro 128++ pseudo-random number generator](http://prng.di.unimi.it) by David Blackman and Sebastino Vigna.

devtools/ci/jenkins/Dockerfile.libcpptraj

@@ -1,10 +1,11 @@
 FROM condaforge/miniforge3
 
+# noninteractive to try and fix tzdata issue
 RUN mkdir /cpptraj && \
     mkdir /.conda /.local && \
     apt-get update && \
     apt-get upgrade -y && \
-    apt-get install -y gfortran gcc g++ bzip2 libfftw3-dev automake make libbz2-dev \
+    DEBIAN_FRONTEND="noninteractive" apt-get install -y gfortran gcc g++ bzip2 libfftw3-dev automake make libbz2-dev \
                        mpich libmpich-dev zlib1g-dev netcdf-bin libnetcdf-dev \
                        liblapack-dev libarpack2-dev
 

devtools/rngtest/Makefile

@@ -0,0 +1,47 @@
+include ../../config.h
+
+#OBJECTS=rngtest.o Random.o RNG.o RNG_Stdlib.o RNG_Marsaglia.o CpptrajStdio.o RNG_MersenneTwister.o RNG_PCG32.o xoshiro128plusplus.o RNG_Xoshiro128pp.o
+OBJECTS=xoshiro128plusplus.o
+SOURCES=rngtest.cpp ../../src/RNG_MersenneTwister.cpp ../../src/RNG.cpp ../../src/CpptrajStdio.cpp ../../src/Random.cpp ../../src/RNG_Stdlib.cpp ../../src/RNG_Marsaglia.cpp ../../src/RNG_PCG32.cpp ../../src/RNG_Xoshiro128pp.cpp
+
+all: rngtest
+
+debug:
+	make CXXFLAGS='-O0 -g' CFLAGS='-O0 -g' rngtest
+
+rngtest: $(SOURCES) $(OBJECTS)
+	$(CXX) $(DIRECTIVES) $(CXXFLAGS) -o rngtest $(SOURCES) $(OBJECTS)
+
+clean:
+	/bin/rm -f $(OBJECTS) rngtest
+
+rngtest.o: rngtest.cpp
+	$(CXX) $(CXXFLAGS) -c -o rngtest.o rngtest.cpp
+
+Random.o: ../../src/Random.cpp
+	$(CXX) $(CXXFLAGS) -c -o Random.o ../../src/Random.cpp
+
+RNG.o: ../../src/RNG.cpp
+	$(CXX) $(CXXFLAGS) -c -o RNG.o ../../src/RNG.cpp
+
+RNG_Stdlib.o: ../../src/RNG_Stdlib.cpp
+	$(CXX) $(CXXFLAGS) -c -o RNG_Stdlib.o ../../src/RNG_Stdlib.cpp
+
+RNG_Marsaglia.o: ../../src/RNG_Marsaglia.cpp
+	$(CXX) $(CXXFLAGS) -c -o RNG_Marsaglia.o ../../src/RNG_Marsaglia.cpp
+
+RNG_MersenneTwister.o: ../../src/RNG_MersenneTwister.cpp
+	$(CXX) $(DIRECTIVES) $(CXXFLAGS) -c -o RNG_MersenneTwister.o ../../src/RNG_MersenneTwister.cpp
+
+RNG_PCG32.o: ../../src/RNG_PCG32.cpp
+	$(CXX) $(CXXFLAGS) -c -o RNG_PCG32.o ../../src/RNG_PCG32.cpp
+
+CpptrajStdio.o: ../../src/CpptrajStdio.cpp
+	$(CXX) $(CXXFLAGS) -c -o CpptrajStdio.o ../../src/CpptrajStdio.cpp
+
+RNG_Xoshiro128pp.o: ../../src/RNG_Xoshiro128pp.cpp
+	$(CXX) $(CXXFLAGS) -c -o RNG_Xoshiro128pp.o ../../src/RNG_Xoshiro128pp.cpp
+
+xoshiro128plusplus.o: ../../src/xoshiro128plusplus.c
+	$(CC) $(CFLAGS) -c -o xoshiro128plusplus.o ../../src/xoshiro128plusplus.c
+

devtools/rngtest/README.md

@@ -0,0 +1,41 @@
+Dieharder Results
+=================
+
+The results from the Dieharder test suite for the various RNGs in cpptraj are in the results.X files. The following tests were run:
+```
+ Test Number	                     Test Name	              Test Reliability
+===============================================================================
+  -d 0  	                  Diehard Birthdays Test	      Good
+  -d 1  	                     Diehard OPERM5 Test	      Good
+  -d 2  	          Diehard 32x32 Binary Rank Test	      Good
+  -d 3  	            Diehard 6x8 Binary Rank Test	      Good
+  -d 4  	                  Diehard Bitstream Test	      Good
+  -d 8  	      Diehard Count the 1s (stream) Test	      Good
+  -d 9  	        Diehard Count the 1s Test (byte)	      Good
+  -d 10  	                Diehard Parking Lot Test	      Good
+  -d 11  	Diehard Minimum Distance (2d Circle) Test	      Good
+  -d 12  	Diehard 3d Sphere (Minimum Distance) Test	      Good
+  -d 13  	                    Diehard Squeeze Test	      Good
+  -d 15  	                       Diehard Runs Test	      Good
+  -d 16  	                      Diehard Craps Test	      Good
+  -d 17  	            Marsaglia and Tsang GCD Test	      Good
+  -d 100  	                        STS Monobit Test	      Good
+  -d 101  	                           STS Runs Test	      Good
+  -d 102  	           STS Serial Test (Generalized)	      Good
+  -d 201  	   RGB Generalized Minimum Distance Test	      Good
+  -d 202  	                   RGB Permutations Test	      Good
+  -d 203  	                     RGB Lagged Sum Test	      Good
+  -d 204  	        RGB Kolmogorov-Smirnov Test Test	      Good
+  -d 205  	                       Byte Distribution	      Good
+  -d 206  	                                 DAB DCT	      Good
+  -d 207  	                      DAB Fill Tree Test	      Good
+  -d 208  	                    DAB Fill Tree 2 Test	      Good
+  -d 209  	                      DAB Monobit 2 Test	      Good
+```
+
+- 0: Marsaglia: 44 failed
+- 1: C stdlib: 37 failed
+- 2: Mersenne Twister (mt19937 from C++ std): 2 failed.
+- 3: Permuted congruential generator 32: 2 failed.
+- 4: Xoshiro128++: 2 failed.
+

devtools/rngtest/RunTest.sh

@@ -0,0 +1,50 @@
+#!/bin/bash
+
+COUNT=100000000
+
+make rngtest
+
+# NOTE: Omitting test 200 for now. Gives following message:
+#Error:  Can only test distribution of positive ntuples.
+#        Use -n ntuple for 0 < ntuple.
+#        Read test description with dieharder -d 200 -h.
+
+TESTNUMS='0 1 2 3 4 8 9 10 11 12 13 15 16 17 100 101 102 201 202 203 204 205 206 207 208 209'
+
+TYPELIST=''
+DIEHARD='no'
+while [ ! -z "$1" ] ; do
+  case "$1" in
+    '-type' ) shift; TYPELIST="$TYPELIST $1" ;;
+  esac
+  shift
+done
+if [ -z "$TYPELIST" ] ; then
+  TYPELIST='0 1 2 3 4'
+  DIEHARD='yes'
+fi
+echo "Type list: $TYPELIST"
+
+for CPPTRAJTYPE in $TYPELIST ; do
+  OUTFILE=results.$CPPTRAJTYPE
+  echo "Cpptraj type $CPPTRAJTYPE"
+  echo "Cpptraj type $CPPTRAJTYPE" > $OUTFILE
+  TMPFILE=temp.$CPPTRAJTYPE
+  ./rngtest -t $COUNT -S 1 -r $CPPTRAJTYPE > $TMPFILE
+  for TEST in $TESTNUMS ; do
+    echo "Test $TEST"
+    dieharder -d $TEST -f $TMPFILE -g 202 >> $OUTFILE
+  done
+  echo ""
+done
+
+if [ "$DIEHARD" = 'yes' ] ; then
+  echo "Diehard numbers"
+  echo "Diehard numbers" > results.diehard
+  dieharder -S 1 -B -o -t $COUNT > diehard.numbers
+  for TEST in $TESTNUMS ; do
+    echo "Test $TEST"
+    dieharder -d $TEST -f diehard.numbers -g 202 >> results.diehard
+  done
+  echo ""
+fi