DL_POLY

DL_POLY is a general-purpose molecular dynamics simulation package. There is the possibility of executing it in parallel or serial mode. This code is capable of simulating up to 30,000 atoms. It can be run parallel on up to 100 processors with good performance. The latest version of DL_POLY (DL_POLY_4) is supplied to individuals under an academic license, free of cost to academic scientists pursuing scientific research of a non-commercial nature. To download the DL_POLY_4 Package, please refer to the web page Registering for the DL_POLY_4 Package.

Homepage:

1. Installation on UBUNTU, by Kianoush Ramezani Shabolaghi:

DL_POLY needs some prerequisites (java, FORTRAN, and mpich). If all of these programs are installed on your system, please skip steps ‎1.1, ‎1.2, and ‎1.3.

1.1 Install Java

sudo su

sudo apt-get update

java -version

sudo apt-get install default-jre

sudo apt-get install default-jdk

sudo apt-get install oracle-java8-installer *

* (Before Running this step, do the following requirements)

***6***:

download jdk-8u162-linux-x64.tar.gz from "https://javaone.ir/java_8" and copy it to /var/cache/oracle-jdk8-installer (in a terminal window you can type: sudo cp -i jdk-8u162-linux-x64.tar.gz /var/cache/oracle-jdk8-installer)

sudo apt-get install oracle-java8-installer

sudo update-alternatives --config java ***

sudo nano /etc/profile

export JAVA_HOME="/usr/lib/jvm/java-...64" *** (End Line)

source /etc/profile

echo $JAVA_HOME

1.2 Install FORTRAN 90 (such as g95)

sudo su

apt-get update

apt-get install gfortran

1.3 Install mpich

sudo su

apt-get update

apt-get install mpich

1.4 Compil and Run DL_POLY_CLASSIC

Execute the following commands in Terminal:

cd source # to ch ory to the source directory

make dlpoly

Copy one of the following files into the source directory (these files are located in the installation directory).

MakePAR - to build a parallel MPI version on a linux platform

MakeSEQ - to build a sequential (one processor) linux version

Make a file in the source directory called “Makefile ”sudo su

Open the “source ” file /span>

make -f Makefile ”

make -f Makefile dlpoly

Once you have installed DL_POLY, you can run an example to verify the installation.

2. Running a test job

Copy DLPOLY.X in the execution directory (such as TEST).

Change the directory to the execution directory and execute the run commands:

./DLPOLY.X CONFIG CONTROL FIELD TABLE ...

For example:

./DLPOLY.X CONFIG CONTROL FIELD

To run with many processors, execute:

mpirun –np * ./DLPOLY.X CONFI CONTROL FIELD

wehere, * is the number of processors.

Note 1: Some files (TABLE and ...) are not mandatory.

Note 2: This program has some supplementary software that can be used to make simulation files (DL_FIELD) and analyze the output data (DL_ANALYSER). Also, some other programs for DFT or Monte Carlo calculations.

Note 3: The execution files of DL_POLY4, and DL_POLY CLASSIC (two versions of DL_POLY) are DL_POLY.Z, and DLPOLY.X, respectively.

DL_MONTE

DL_MONTE is a general-purpose parallel Monte Carlo simulation package. One of the objectives of DL_MONTE-2 is to provide an alternative (Monte Carlo) methodology for users of DL POLY. Inputs to both programs are arranged via three compulsory input files: CONFIG, CONTROL, and FIELD. DL_MONTE-2. It also uses the same internal units as DL_POLY. One can run DL_MONTE to obtain: adsorption isotherms, the liquid-vapor coexistence curve (phase diagram), umbrella sampling, and many other data.

Homepage:

https://www.ccp5.ac.uk/DL_MONTE

Examples:

https://dl_monte.gitlab.io/dl_monte-tutorials-pages/index.html <

Compiling DL_MONTE in parallel version (MPI version):

Open Terminal in your download folder and execute:

./build: PRL dir mpi

After running the above command, a new directory “bin ” will be created containing the DL_MONTE executable fil (DLMONTE-PRL-VDW_dir.X and DLMONTE-PRL.X)

Now, DL_MONTE is installed, and one can run the simulations.

3. Run a DL_MONTE test job

To run a DL_MONTE job, one should have the CONFIG, FIELD, and CONTROL files. Copy DLMONTE-PRL.X in your working directory and type the following command:

mpirun –np * ./DLMONTE-PRL.X CONF IG CONTROL FIELD

where * is the number of processors