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WebMO - Computational chemistry on the WWW
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November 20, 2017
Computational Chemistry Pre-Compiled Binaries for Linux

Pre-compiled binaries of computational chemistry programs can save the time and trouble of obtaining and compiling the program source code.

When using a pre-compiled binary, be aware that one must use a binary that is appropriate for one's particular hardware (e.g., x86 or ia32, Intel x86_64 or EM64T or Intel64, AMD x86_64 or Opteron, SGI MIPS R10000, etc.), operating system, (e.g., Linux, OS X, Windows, IRIX, AIX, Solaris, etc.), bitsize (32-bit or i4, 64-bit or i8), distribution/vendor (e.g., RHEL, CentOS, Fedora Core, RedHat, SuSE, SGI, Solaris, etc.), and version (4, 6.2, 7.2, 11, etc.).

GAMESS

GAMESS is currently no longer available for Linux as a pre-compiled binary, although it is available for other OS's. You must compile the source code on linux using a system compiler, e.g., f77, gfortran, or another popular compiler.

GAUSSIAN 09

  1. Obtain Gaussian 09
    Gaussian 09 is a commercial software product and must be purchased from Gaussian, Inc. Both source code and pre-compiled binary versions of Gaussian 09 are available.
  2. Setup gaussian group and add authorized users to this group
    $ su
    # cd /etc
    # cp -p group group.bak
    # cp -p gshadow gshadow.bak
    # grep 499 group
    # groupadd -g 499 gaussian
    # usermod -a -G gaussian webmo
    # usermod -a -G gaussian smith
    # usermod -a -G gaussian jones
  3. Copy binary distribution from CD-ROM
    # mount /mnt/cdrom
    # cd /usr/local
    # cp -p /mnt/cdom/tar/*.TGZ .
    # umount /mnt/cdrom
  4. Extract files
    # tar xzvf *.TGZ
    # chown -R root:gaussian g09
    # exit
  5. Run a test job from the command line
    $ cd ~
    $ mkdir g09
    $ cd g09
    $ vi g09setup
          export g09root=/usr/local
          export GAUSS_SCRDIR=/tmp
          source $g09root/g09/bsd/g09.profile
    $ cp -p /usr/local/g09/tests/com/test0001.com test0001.com
    $ cp -p /usr/local/g09/tests/amd64/test0001.log test0001.log.amd64
    $ source g09setup
    $ g09 < test0001.com > test0001.log.linux
    $ tail test0001.log.amd64
    $ tail test0001.log.linux
  6. Configure WebMO to use Gaussian09 as a computational engine
    • Login to WebMO as user 'admin'
    • Click 'Interface Manager' to enable the interfaces to any computational chemistry packages that you have installed on your system
    • Click the 'Enable' button for Gaussian
    • Click 'Edit' to configure the Gaussian interface
    • Verify that the first two entries are correct:
      • Gaussian Version: Gaussian 09
      • Gaussian root directory: /usr/local
    • Click the 'Suggest' button to fill the remining entries
    • Click the 'Submit' button for the changes to take effect
    • Click 'Return', 'Return to Admin', and 'Logout' to exit the WebMO administration page
  7. Login as a WebMO user, and run a test job using Gaussian as the computational engine
MOLPRO 2015

  1. Obtain a Molpro license
    MolPro is a commercial software product, and a license must be purchased from www.molpro.net. Registered licensees will receive a Molpro username and password, which grant access to the download area of the Molpro website.
  2. Download the Molpro binary and license token
    At the Molpro website, follow the "Log in" link, and supply your Molpro username and password. Follow the "Account information and ordering" link. Download a copy of the license token. Follow the "Download" link. Download the latest binary version appropriate for your hardware architecture and operating system, for example, molpro-mpp-2015.1.18.linux_x86_64_openmp.sh.gz for 64-bit Linux. (Note that mpp versions will run on a single processor as well as in parallel.)
  3. Install the molpro binary
    $ su -
    # mkdir /tmp/molpro
    # cd /tmp/molpro
    # cp -p {download_dir}/molpro-mpp-2015.1.18.linux_x86_64_openmp.sh.gz .
    # gunzip molpro-mpp-2015.1.18.linux_x86_64_openmp.sh.gz
    # chmod 755 molpro-mpp-2015.1.18.linux_x86_64_openmp.sh
    # mkdir /usr/local/molpro         <--WebMO standard location
    # ./molpro-mpp-2015.1.18.linux_x86_64_openmp.sh
    # Enter bin directory to link Molpro (optional) []
    /usr/local/molpro
    Enter installation directory for Molpro files [/usr/local/molpro/molprop_2015_1_linux_x86_64_i8]
    Installation of Molpro files complete
    Please give your username for accessing molpro
    ******
    Please give your password for accessing molpro
    ******
    Token sucessfully downloaded and installed
  4. If Molpro license token was not automatically installed in last step, install license token manually
    # cp {download_dir}/token.txt /usr/local/molpro/molprop_2015_1_linux_x86_64_i8/lib/.token
    # chmod 644 /usr/local/molpro/molprop_2015_1_linux_x86_64_i8/lib/.token
  5. In necessary, fix file ownerships
    # chown -R root:root /usr/local/molpro
  6. Clean up
    # rm -rf /tmp/molpro/
    # exit
  7. Run a test job from the command line
    $ cd ~
    $ mkdir test
    $ cd test
    $ cp -p /usr/local/molpro/molprop_2015_1_linux_x86_64_i8/examples/procedures .
    $ cp -p /usr/local/molpro/molprop_2015_1_linux_x86_64_i8/examples/h2o_optmp2.com .
    $ /usr/local/molpro/molpro h2o_optmp2.com
    $ ls -alF h2o*
  8. Configure WebMO to use Molpro as a computational engine
    • Login to WebMO as user 'admin'
    • Click 'Interface Manager' to enable the interfaces to any computational chemistry packages that you have installed on your system
    • Click the 'Enable interface' icon for Molpro
    • Click the 'Edit interface' icon to configure the Molpro interface
    • Verify that the entries are correct; if necessary, edit entries and click 'Submit'
      • Molpro version: 2015.1
      • Molpro path: /usr/local/molpro/molpro
      • LD library directory:
      • Cores: Min=1, Max=1, Default=1 (Pro only; more according to architecture)
    • Click 'Return', 'Return to Admin', and 'Logout' to exit the WebMO administration page
  9. Login as a WebMO user, and run a test job using Molpro as the computational engine
  10. Notes:
MOPAC 7

  1. Obtain the MOPAC 7 binary
    MOPAC 7 is public domain and the pre-compiled binary code mopac7.exe.tar.gz can be obtained from the WebMO website
  2. Uncompress the archive
    $ su
    # cd /usr/local
    # tar xzvf /{download_dir}/mopac7.exe.tar.gz
    # chown -R root:root mopac7
    # exit
  3. Configure WebMO to use MOPAC7 as a computational engine
    • Login to WebMO as user 'admin'
    • Click 'Interface Manager' to enable the interfaces to any computational chemistry packages that you have installed on your system
    • Click the 'Enable' button for MOPAC
    • Click 'Edit' to configure the MOPAC interface
    • Verify that the entries are correct; if necessary, edit entries and click Submit
      • Mopac version: Mopac 7
      • Mopac path: /usr/local/mopac7/mopac.exe
      • External parameter dir:
    • Click 'Return', 'Return to Admin', and 'Logout' to exit the WebMO administration page
  4. Login as a WebMO user, and run a test job using MOPAC as the computational engine
MOPAC 2016

  1. Visit the MOPAC homepage at openmopac.net and request an academic license for MOPAC. After a few days, you should receive a license key of the form 12345678a12345678
  2. Download the 64-bit linux version of MOPAC2016
  3. Make sure you have unzip installed
    $ sudo yum install unzip (for CentOS)
    $ sudo apt-get install unzip (for Debian, Ubuntu)
  4. Unzip the archive
    $ sudo su -
    # mkdir /usr/local/mopac2016/
    # cd /usr/local/mopac2016/
    # unzip /{download_dir}/MOPAC2016_for_Linux_64_bit.zip
  5. Install the library
    # cp -p libiomp5.so /usr/lib/
  6. Change permissions on mopac
    # chmod 755 MOPAC2016.exe
  7. Run MOPAC2016.exe, passing in the license key you recieved from Mr MOPAC. Follow on-screen prompts to accept the license.
    # export MOPAC_LICENSE=/usr/local/mopac2016
    # ./MOPAC2016.exe license
    # exit
  8. Run a test job from the command line
    $ cd ~
    $ mkdir -p test/mopac2016/
    $ cd test/mopac2016/
    $ cp "/usr/local/mopac/Example data set.mop" .
    $ export MOPAC_LICENSE=/usr/local/mopac2016
    $ /usr/local/mopac2016/MOPAC2016.exe "Example data set.mop"
    $ more "Example data set.out"
  9. Configure WebMO to use MOPAC as a computational engine
    • Login to WebMO as user 'admin'
    • Click 'Interface Manager' to enable the interfaces to any computational chemistry packages that you have installed on your system
    • Click the 'Enable' button for MOPAC
    • Click 'Edit' to configure the MOPAC interface
    • Verify that the entries are correct; if necessary, edit entries and click Submit
      • Mopac version: Mopac 2016
      • Mopac path: /usr/local/mopac2016/MOPAC2016.exe
      • External parameter dir:
    • Click 'Return to Admin', followed by 'Logout' to exit the WebMO administration page
  10. Login as a WebMO user, and run a test job using MOPAC as the computational engine
  11. Documentation can be found at openmopac.net/manual.
NWCHEM 5.5

  1. Request a copy of the NWChem binary
    Visit the NWChem homepage and request a copy of NWChem from their download page. Create an EMSL user account by using the EMSL User Portal web-based registration form, and the temporary password send to your email address. Upon logging in to the EMSL User Portal, select Usage Type: Software Agreement and click Register for New Software. Fill out the Software User Info, choose to download NWChem (and possibly ECCE), and digitally sign the Software End User Agreement. After a few days, your request will be processed and your software agreement status will change from "pending" to "approved" if your meet the EMSL criteria (e.g., permanent faculty member/researcher in non-embargoed country).
  2. Download NWChem binary
    Visit the NWChem homepage and request a copy NWChem from their download page. Upon logging in to the EMSL User Portal with your email address and password specified above, select Usage Type: Software Agreement. Choose NWChem download, Binaries, and the latest version. Download the NWChem binary appropriate for your computer architecture (e.g., nwchem-5.1.1-LINUX64-RHELWS4-ifort-AMD64.tgz for 64-bit Linux running on an Opteron processor).
  3. Untar the binary files
    A summary of this procedure is available in the INSTALL.binbuilds file. Detailed instructions follow:
    $ su
    # cd /usr/local
    # mkdir nwchem-5.1.1
    # cd nwchem-5.1.1
    # tar xzf {download_dir}/nwchem-5.1.1-LINUX64-RHELWS4-ifort-AMD64.tgz
    # chown -R root:root /usr/local/nwchem-5.1.1
    # chmod 755 /usr/local/nwchem-5.1.1/bin/*
    # chmod 755 /usr/local/nwchem-5.1.1/etc/
  4. Make a default.nwchemrc file
    # cd /usr/local/nwchem-5.1.1/etc
    # ./gen_default.nwchemrc
  5. Define this version of NWChem as the default with a symbolic link
    # cd /usr/local
    # ln -s nwchem-5.1.1 nwchem
    # exit
  6. Run test job from the command line
    $ cd ~
    Specify the location of the nwchem with either
          $ ln -s /usr/local/nwchem/data/default.nwchemrc .nwchemrc
    or
          $ export NWCHEM_BASIS_LIBRARY=/usr/local/nwchem/usr.local.lib.nwchem/libraries/
    $ mkdir ~/nwchem
    $ cd ~/nwchem
    $ cp -p /usr/local/nwchem/examples/h2o/h2o.nw .
    $ /usr/local/nwchem/bin/nwchem h2o.nw > h2o.out
    $ more h2o.out
  7. Configure WebMO to use NWChem as a computational engine
    • Login to WebMO as user 'admin'
    • Click 'Interface Manager' to enable the interfaces to any computational chemistry packages that you have installed on your system
    • Click the 'Enable' button for NWChem
    • Click 'Edit' to configure the NWChem interface
    • Verify that the entries are correct; if necessary, edit entries and click 'Submit'
      • NWChem Version: 5.1.1
      • NWChem directory: /usr/local/nwchem
      • NWChem binary: /usr/local/nwchem/bin/nwchem
      • NWChem config file: /usr/local/nwchem/etc/default.nwchemrc
    • Click 'Return', 'Return to Admin', and 'Logout' to exit the WebMO administration page
  8. Login as a WebMO user, and run a test job using NWChem as the computational engine
  9. Notes
ORCA3

  1. Obtain Orca
    Orca is available free of charge for academic use. Obtain by making an account at Orca Forums and downloading most recent version of orca 3 for linux in *.tbz format
  2. Install bzip2
    # yum install bzip2
  3. Extract files (replace X_X_X with current version number)
    # cd /usr/local
    # tar xjf {download_dir}/orca_X_X_X_linux_x86-64.tbz
    # chown -R root:root orca_X_X_X_linux_x86-64/
    # exit
  4. Run a test job from the command line
    • Make a directory to hold test files
      $ cd ~
      $ mkdir orca
      $ cd orca/
    • Make a new file called h2o.inp containing the following:
      ! B3LYP def2-SVP Opt
      *xyz 0 1
      O 0.000000000 0.000000000 0.000000000
      H 0.000000000 0.759337000 0.596043000
      H 0.000000000 -0.759337000 0.596043000
      *
    • Run Orca using the file as input
      $ /usr/local/orca_3_0_3_linux_x86-64/orca h2o.inp >h2o.out
      $ more h2o.out
  5. Configure WebMO to use Orca as a computational engine
    • Login to WebMO as user 'admin'
    • Click 'Interface Manager' to enable the interfaces to any computational chemistry packages that you have installed on your system
    • Click the 'Enable' button for ORCA
    • Click 'Edit' to configure the Orca interface
    • Verify that the first two entries are correct (replace X's with current version):
      • ORCA version: X.X.X
      • ORCA directory: /usr/local/orca_X_X_X_linux_x86-64
    • Click the 'Submit' button for the changes to take effect
    • Click 'Return', 'Return to Admin', and 'Logout' to exit the WebMO administration page
  6. Login as a WebMO user, and run a test job using Orca as the computational engine
PQS 3.3

  1. Download PQS binary
    Visit the PQS homepage and download a copy of PQS from their software page. Choose an appropriate implementation and architecture, or choose the free 32-bit trial version, e.g., pqs_mpi2-3.3-19.i386.tar.gz. The following instructions are based on a TAR file download, not the RPM download.
  2. Untar the binary files
    $ su
    # cd /tmp
    # tar xzf {download_dir}/pqs_mpi2-3.3-19.i386.tar.gz
    # cd pqs_trial-3.3-19.i386
    # ./install.sh
    Please choose the installation type: 1 Multi-user install (requires root privileges)
    Enter the target directory for PQS install [/usr/local/share/PQS]: /usr/local/PQS
    Enter the scratch directory for PQS jobs [/scr]: /tmp
    Please choose one of the following actions: 1 Skip this step leaving PQS_SCRDIR = /tmp
    Now you can choose to create links to the PQS scripts. Do you want to proceed [y]: n
  3. Fix file ownerships
    # chown -R root:root /usr/local/PQS
  4. Clean up
    # cd /tmp
    # rm -rf pqs_trial-3.3-19.i386
    # exit
  5. Configure WebMO to use PQS as a computational engine
    • Login to WebMO as user 'admin'
    • Click 'Interface Manager' to enable the interfaces to any computational chemistry packages that you have installed on your system
    • Click the 'Enable' button for PQS
    • Click 'Edit' to configure the PQS interface
    • Verify that the entries are correct; if necessary, edit entries and click 'Submit'
      • PQS version: 3.3
      • PQS directory: /usr/local/PQS-3.3trial
      • PQS binary: /usr/local/PQS-3.3trial/pqs.x
    • Click 'Return', 'Return to Admin', and 'Logout' to exit the WebMO administration page
  6. Login as a WebMO user, and run a test job using PQS as the computational engine
PSI4

  1. Make sure you have bzip2 installed
    $ sudo yum install bzip2 (for CentOS)
    $ sudo apt-get install bzip2 (for Debian, Ubuntu)
  2. Download the miniconda installer
    $ sudo su -
    # cd /tmp/
    # curl -o Miniconda-latest.sh "https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh"
  3. Install miniconda
    # ./Miniconda-latest.sh -b -p /usr/local/miniconda
  4. Include miniconda in your path
    # export PATH=/usr/local/miniconda/bin:$PATH
  5. Update miniconda
    # conda update --yes --all
  6. Add psi4 to miniconda's channels
    # conda config --add channels http://conda.anaconda.org/psi4
  7. Install psi4
    # conda install --yes psi4
    # exit
  8. Run a test job from the command line
    $ cd ~
    $ mkdir -p test/psi4/
    $ cd test/psi4/
    $ cp /usr/local/miniconda/share/psi4/samples/stability1/input.dat .
    $ export PATH=/usr/local/miniconda/bin:$PATH
    $ psi4 input.dat
    $ more output.dat
  9. Configure WebMO to use psi4 as a computational engine
    • Login to WebMO as user 'admin'
    • Click 'Interface Manager' to enable the interfaces to any computational chemistry packages that you have installed on your system
    • Click the 'Enable' button for PSI4
    • Click 'Edit' to configure the PSI4 interface
    • Verify that the entries are correct; if necessary, edit entries and click Submit
      • Psi version: 4.0
      • Psi directory: /usr/local/miniconda/
    • Click 'Return to Admin', followed by 'Logout' to exit the WebMO administration page
  10. Login as a WebMO user, and run a test job using Psi4 as the computational engine
QCHEM 4.X

  1. Download the QChem installer
    # wget -N http://www.q-chem.com/download/qcinstall/qcinstall.sh
    # chmod +x qcinstall.sh
  2. Run the installer, specifying the following options when prompted
    # ./qcinstall.sh
          n
          /usr/local/qchem
          1
          /scratch (or path to your scratch directory)
          n
          (enter to use ssh)
          (enter to use default memory limit)
  3. Obtain a license
    # /usr/local/qchem/qcinstall.sh --update-lic
    Follow the prompts to obtain a license
    When emailed a license, save it as /usr/local/qchem/qcaux/license/qchem.license.dat
  4. Run a test job from the command line
    • Make a directory to hold test files and set up the environment
      $ cd ~
      $ mkdir qchem
      $ cd qchem/
      $ source /usr/local/qchem/qcenv.sh
    • Copy in a sample job
      $ cp -p /usr/local/qchem/samples/freq/hf_h2o.in .
    • Run Q-Chem using the file as input
      $ /usr/local/qchem/bin/qchem hf_h2o.in >hf_h2o.out
      $ more hf_h2o.out
  5. Configure WebMO to use Q-Chem as a computational engine
    • Login to WebMO as user 'admin'
    • Click 'Interface Manager' to enable the interfaces to any computational chemistry packages that you have installed on your system
    • Click the 'Enable' button for QChem
    • Click 'Edit' to configure the QChem interface
    • Verify that the first two entries are correct (replace X's with current version):
      • QChem version: X.X
      • QChem directory: /usr/local/qchem
    • Click the 'Submit' button for the changes to take effect
    • Click 'Return', 'Return to Admin', and 'Logout' to exit the WebMO administration page
  6. Login as a WebMO user, and run a test job using QChem as the computational engine
QUANTUM ESPRESSO

  1. Visit the quantum espresso download page and download the latest espresso-X.X.X.tar.gz file
  2. Install gfortran and make
  3. $ sudo yum install gcc-gfortran make (for CentOS)
    $ sudo apt-get install gfortran make (for Debian, Ubuntu)
  4. Unzip the source code to /usr/local/
  5. $ sudo su -
    # cd /usr/local/
    # tar xzf /path/to/espresso-X.X.X.tar.gz
  6. Compile quantum espresso
  7. # cd espresso-X.X.X/
    # ./configure
    # make all
  8. Run a test job from the command line
  9. # cd PW/examples/example01/
    # ./run_example
    # cd results/
    # less al.band.cg.out
  10. Enable quantum espresso in WebMO
    • Login to WebMO as user 'admin'
    • Click 'Interface Manager' to enable the interfaces to any computational chemistry packages that you have installed on your system
    • Click the 'Enable' button for Quantum Espresso
    • Click 'Edit' to configure the Quantum Espresso interface
    • Verify that the entries are correct; if necessary, edit entries and click Submit
      • PWSCF Version: X.X.X
      • PWSCF bin directory: /usr/local/espresso-X.X.X/bin
      • PWSCF pseudopotential directory: /usr/local/espresso-X.X.X/pseudo
      • Use MPI: (unchecked)
    • Click 'Return to Admin', followed by 'Logout' to exit the WebMO administration page
  11. Quantum espresso jobs use pseudopotentials, which must be downloaded separately. These should be downloaded from www.quantum-espresso.org/pseudopotentials/ and placed in /usr/local/espresso-X.X.X/pseudo/

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