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UB CCR new software instructions
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| <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd"> | ||
| <html> | ||
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| <head> | ||
| <title>The Akimov Research Group</title> | ||
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| <meta charset="utf-8"> | ||
| <meta name="viewport" content="width=device-width, initial-scale=1"> | ||
| <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.1.0/css/bootstrap.min.css"> | ||
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| <script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.14.0/umd/popper.min.js"></script> | ||
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| <!-- Global site tag (gtag.js) - Google Analytics --> | ||
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| <body> | ||
| <!-- Navigation bar style="margin-top:-2px;" --> | ||
| <nav class="navbar navbar-expand-sm bg-dark navbar-dark fixed-top"> | ||
| <ul class="navbar-nav"> | ||
| <li class="nav-item"><a class="nav-link" href="../index.html">Home</a></li> | ||
| <li class="nav-item"><a class="nav-link" href="../research.html">Research</a></li> | ||
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| <li class="nav-item active"><a class="nav-link" href="../soft_and_tuts.html">Software & Tutorials</a></li> | ||
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| <xmp theme="bootstrap"> | ||
| # 3.1. CP2K on UB CCR | ||
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| [CP2K](https://www.cp2k.org/) is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. CP2K provides a general framework for different modeling methods such as DFT using the mixed Gaussian and plane waves approaches GPW and GAPW. Supported theory levels include DFTB, LDA, GGA, MP2, RPA, semi-empirical methods (AM1, PM3, PM6, RM1, MNDO, …), and classical force fields (AMBER, CHARMM, …). CP2K can do simulations of molecular dynamics, metadynamics, Monte Carlo, Ehrenfest dynamics, vibrational analysis, core level spectroscopy, energy minimization, and transition state optimization using NEB or dimer method. (Detailed overview of features.) | ||
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| ## A. Installation | ||
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| To install CP2K, we use the instruction in [here](https://github.com/cp2k/cp2k/blob/master/INSTALL.md) and a recipe for installing it on UB CCR using GNU compilers is provided below. For compilation using Intel compiler see [this link](https://github.com/compchem-cybertraining/Tutorials_CP2K/blob/master/INSTALLATION.md). | ||
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| git clone --recursive -b support/v2024.1 https://github.com/cp2k/cp2k.git cp2k | ||
| cd cp2k/tools/toolchain | ||
| module load gcc/11.2.0 | ||
| module load openmpi/4.1.1 | ||
| module load imkl/2022.0.1 | ||
| module load cmake/3.22.1 | ||
| ./install_cp2k_toolchain.sh --with-gcc=system --with-mkl=system --with-cmake=system --with-sirius=no --with-openmpi=system | ||
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| In order to see more options you can type `./install_cp2k_toolchain.sh --help`. Then, the toolchain will download and install the necessary files and create arch files in the install directory. Copy and paste the arch files to the `cp2k/arch` directory by: | ||
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| ``` | ||
| cp install/arch/local* ../../arch/. | ||
| ``` | ||
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| In order to `make` CP2K, do the following commands: | ||
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| ``` | ||
| source install/setup # You need to source this file in the install directory before installation | ||
| cd ../.. | ||
| make -j 16 ARCH=local VERSION=psmp | ||
| ``` | ||
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| After compilation is finished, create a module file in the modules directory (`/projects/academic/cyberwksp21/MODULES`) with the following content: | ||
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| ``` | ||
| whatis("Description: CP2K") | ||
| whatis("Version: 2024.1") | ||
| whatis("Category: Chem") | ||
| load("ccrsoft/2023.01") | ||
| load("imkl/2022.0.1") | ||
| load("gcc/11.2.0") | ||
| load("openmpi/4.1.1") | ||
| prepend_path("PATH","/projects/academic/cyberwksp21/SOFTWARE_NEW_ENV/cp2k/cp2k_v24/exe/local") | ||
| prepend_path("LD_LIBRARY_PATH","/cvmfs/soft.ccr.buffalo.edu/versions/2023.01/easybuild/software/Core/imkl/2022.0.1/mkl/2022.0.1/lib/intel64") | ||
| prepend_path("LD_LIBRARY_PATH","/cvmfs/soft.ccr.buffalo.edu/versions/2023.01/easybuild/software/avx512/Compiler/gcc/11.2.0/openmpi/4.1.1/lib64") | ||
| prepend_path("LD_LIBRARY_PATH","/cvmfs/soft.ccr.buffalo.edu/versions/2023.01/easybuild/software/Core/gcccore/11.2.0/lib64") | ||
| setenv("OMP_NUM_THREADS","1") | ||
| add_property("type_","chem") | ||
| ``` | ||
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| ## B. Running CP2K | ||
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| See the following script for an example of running a computation with CP2K. | ||
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| Here is an example to run on our cluster: | ||
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| #!/bin/sh | ||
| #SBATCH --partition=general-compute --qos=general-compute | ||
| #SBATCH --clusters=ub-hpc | ||
| #SBATCH --nodes=1 | ||
| #SBATCH --ntasks-per-node=6 | ||
| #SBATCH --cpus-per-task=1 | ||
| #SBATCH --time=00:10:00 | ||
| #SMATCH --mem=10000 | ||
| ###SBATCH -C CPU-E5-2650v4 # This is the type of CPUs on valhalla nodes | ||
| #SBATCH -C CPU-Gold-6130 # The head node CPU type for not getting warnings or errors | ||
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| module use /projects/academic/cyberwksp21/MODULES | ||
| module load cp2k/v24/avx512 | ||
| mpirun -np 6 cp2k.psmp -i input.inp -o out | ||
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| ## C. Input Example | ||
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| ### C.1. Single point calculations of water molecule at the B3LYP level of theory: | ||
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| ``` | ||
| &GLOBAL | ||
| # TRACE | ||
| PRINT_LEVEL MEDIUM | ||
| PROJECT H2O-hybrid-b3lyp_libxc | ||
| &END GLOBAL | ||
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| &FORCE_EVAL | ||
| METHOD Quickstep | ||
| &DFT | ||
| BASIS_SET_FILE_NAME EMSL_BASIS_SETS | ||
| POTENTIAL_FILE_NAME POTENTIAL | ||
| &MGRID | ||
| CUTOFF 250 | ||
| REL_CUTOFF 50 | ||
| &END MGRID | ||
| &POISSON | ||
| PERIODIC NONE | ||
| PSOLVER MT | ||
| &END POISSON | ||
| &QS | ||
| METHOD GAPW | ||
| &END QS | ||
| &SCF | ||
| EPS_SCF 1.0E-6 | ||
| IGNORE_CONVERGENCE_FAILURE | ||
| MAX_SCF 2 | ||
| SCF_GUESS ATOMIC | ||
| &END SCF | ||
| #This is B3LYP using VWN3 | ||
| &XC | ||
| &HF | ||
| FRACTION 0.20 | ||
| !&MEMORY | ||
| ! MAX_MEMORY 5 | ||
| !&END MEMORY | ||
| &SCREENING | ||
| EPS_SCHWARZ 1.0E-10 | ||
| &END SCREENING | ||
| &END HF | ||
| &XC_FUNCTIONAL | ||
| &HYB_GGA_XC_B3LYP | ||
| &END HYB_GGA_XC_B3LYP | ||
| &END XC_FUNCTIONAL | ||
| &END XC | ||
| &END DFT | ||
| &SUBSYS | ||
| &CELL | ||
| ABC 6.0 6.0 6.0 | ||
| PERIODIC NONE | ||
| &END CELL | ||
| &COORD | ||
| O 0.000000 0.000000 -0.065587 | ||
| H 0.000000 -0.757136 0.520545 | ||
| H 0.000000 0.757136 0.520545 | ||
| &END COORD | ||
| &KIND H | ||
| BASIS_SET 6-31Gxx | ||
| POTENTIAL ALL | ||
| &END KIND | ||
| &KIND O | ||
| BASIS_SET 6-31Gxx | ||
| POTENTIAL ALL | ||
| &END KIND | ||
| &END SUBSYS | ||
| &END FORCE_EVAL | ||
| ``` | ||
| </xmp> | ||
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| </body> | ||
| </html> |
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