Tag: CP2K

Periodic and non-periodic box

 I’m new in CP2K and my question are: 1) Is there any way to print out the xyz file with the molecules ordered inside the box because every time I run, it always print out in an unordered way and to make it ordered I have to wrap it via…

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Molecular Dynamics Software Market Size, Historical Growth, Analysis, Opportunities and Forecast To 2026

The Molecular Dynamics Software market research focuses on the major economic changes that are projected to occur between 2022 and 2028. The primary focus of analysis is on factors that may influence how the firm sector progresses, such as growth boosters, inhibitors, and other potential opportunities. According…

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howto:geometry_optimisation [CP2K Open Source Molecular Dynamics ] (2022)

Introduction This tutorial is designed to illustrate how to relax the structureof a system (without changing the cell dimensions) using CP2K. Weuse the relaxation of a water (H\(_2\)O) molecule as an example. The example files are contained in geometry_optimisation.tgz that comes with this tutorial. The calculation was carried out with…

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cp2k-common – Fedora Packages

cp2k-common – Fedora Packages Molecular simulations software – common files CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT)…

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Gromacs 2021 + cp2k – User discussions

GROMACS version: 2021.2GROMACS modification: No Hello GROMACS users and developers. I have a demand to compile GROMACS 2021.2 with CP2K 9.1. Is this combination supported? If so, how to do it? I noticed that the cmake variables DGMX_CP2K, DCP2K_DIR and DCP2K_LINKER_FLAGS are available only in the 2022 version. And from…

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U.S Bioinformatics Software Market 2022

Bioinformatics Software Market Report: 2022-2027 Bioinformatics Software Market (Newly published report) which covers Market Overview, Future Economic Impact, Competition by Manufacturers, Supply (Production), and Consumption Analysis The market research report on the global Bioinformatics Software industry provides a comprehensive study of the various techniques and materials used in the production…

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Molecular Dynamics Software market share from APAC, Europe, America application to rise at XX% CAGR through 2028

added a new report on Molecular Dynamics Software market with respect to the pivotal drivers influencing the revenue graph of this business sphere. The current trends of Molecular Dynamics Software market in conjunction with the geographical landscape, demand spectrum, remuneration scale, and growth graph of this vertical…

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Molecular Dynamics Simulation Software Market by 2029

New Jersey (United States) – A2Z Market Research published new research on Global Molecular Dynamics Simulation Software covering the micro-level of analysis by competitors and key business segments (2022-2029). The Global Molecular Dynamics Simulation Software explores a comprehensive study on various segments like opportunities, size, development, innovation, sales, and overall…

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main-i386-default][science/cp2k] Failed for cp2k-9.1.0 in configure

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: beefy17.nyi.freebsd.org/data/main-i386-default/p429f3de9bdcd_s2573e6ced9/logs/cp2k-9.1.0.log Build URL: beefy17.nyi.freebsd.org/build.html?mastername=main-i386-default&build=p429f3de9bdcd_s2573e6ced9 Log: =>> Building science/cp2k build started at Sat Jun 4…

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Molecular Dynamics Software Market Growing Popularity & Emerging Trends

The latest independent research document on Molecular Dynamics Software examine investment in Market. It describes how companies deploying these technologies across various industry verticals aim to explore its potential to become a major business disrupter. The Molecular Dynamics Software study eludes very useful reviews & strategic assessment including the generic market…

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Bioinformatics Software Market Outlook: Post Covid-19 Scenario by 2029

California (United States) – The Bioinformatics Software Market Research Report is a professional asset that provides dynamic and statistical insights into regional and global markets. It includes a comprehensive study of the current scenario to safeguard the trends and prospects of the market. Bioinformatics Software Research reports also track future…

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GROMACS+CP2K Single vs Double Precision – User discussions

cbl123 April 4, 2022, 8:38pm #1 GROMACS version: 2022GROMACS modification: Yes/No (CP2K) Hello dear users and devs, I would like to know if there’s major implications in the accuracy of my calculations if I use single precision instead of the recommended double precision for QM/MM calculations with Gromacs 2022+CP2K. Thanks…

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Nvt.mdp killed in 7 min – User discussions

GROMACS version:2022+cp2k interface basically, my system is small but I couldn’t start nvt job. Can you I help me, what I am doing wrong?Thank you in advance I am taking that error : Command line:gmx_cp2k mdrun -s nvt.tpr -v -deffnm nvt Compiled SIMD: AVX_256, but for this host/run AVX2_256 might…

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Nvt.tpr -I couldn’t manage my nvt.tpr – User discussions

GROMACS version:2022-cp2k interface I couldn’t manage my nvt.tpr I tried to fix problem but I couldn’t. gmx_cp2k grompp -f nvt.mdp -c confout.gro -r confout.gro -p topol.top -n index.ndx -o nvt.tpr nvt.mdb file :; md-nvt.mdp – used as input into grompp to generate nma-nvt.tprintegrator = md ; MD using leap-frog integratordt…

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CP2K related software dev postdoc positions available in the UK

please have a look if you might be interested – I’ll post directly below here as well. Timescale, as ever, is tight. Do send emails if you might be interested. Subject: Extended deadline – computational scientist positions at STFC (UK) Senior Computational Scientists – Accelerator Development and Multiscale Workflows Science…

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Weird movement of Pt (fcc 111) layers with one OH radical on top

Dear CP2K users, I am performing geometry optimizations for Pt slab (fcc111) with one hydroxyl (OH) radical on top. First, the cell optimization of bulk Pt (fcc111) is performed and successfully converged (Pt_cellopt.xyz).  However, when I put one OH radical on Pt 111 to perform geometry optimization, I observed a…

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CP2K – Universitetet i Oslo

CP2K is a program to perform atomistic and molecular simulations of solid state, liquid, molecular, and biological systems. Description CP2K is a program to perform atomistic and molecular simulations of solid state, liquid, molecular, and biological systems. It provides a general framework for different methods such as e.g., density functional…

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TIP4P/2005f implementation

Hi, I was trying to implement TIP4P/2005f force field in CP2K. I have setup the relevant forcefield and geometry section in the following manner: &FORCE_EVAL  METHOD FIST  &MM    &FORCEFIELD      &SPLINE        EMAX_SPLINE 1.0E+128        RCUT_NB 12.0      &END SPLINE      &BEND   …

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Electronic Structure Calculation

Hi All, I have tried electronic structure calculation exercise given in cp2k exercises. The link is given below. But, the input file is not running and showing error like,  ‘sys.c:744  MXM  WARN  Conflicting CPU frequencies detected, using: 2015.75 [1644570133.051452] [master:22512:0]         mxm.c:196  MXM  WARN  The ‘ulimit -s’…

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ambmax00/cp2k – Giters

CP2K 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….

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Error in print &molecular_dipoles under &LOCALIZE in cp2k

May I ask how to print the dipole moment per molecule of the system in cp2k? I tried to do print molecular_dipoles in LOCALIZE:    &LOCALIZE       METHOD CRAZY       USE_HISTORY       &PRINT         &MOLECULAR_DIPOLES           FILENAME…

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CP2K version 9.1 released

Dear CP2K users, we are pleased to announce the release of the CP2K version 9.1 (December 31, 2021). The CP2K source tarball and a pre-compiled binary can be downloaded from:   github.com/cp2k/cp2k/releases/tag/v9.1.0 Further information about Git access and Linux distros can be found at:   www.cp2k.org/download The corresponding input description…

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speed slow down on running CP2K

Dear All I am newbie in CP2K and trying to run MD simulation on the benzene-water cluster with BLYP functional. I found a strange phenomenon when I check one of the NVE output files with the filename extension of .ener. The CPU time slowed down significantly after step 12283 and…

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main-armv7-default][science/cp2k-data] Failed for cp2k-data-7.1.0 in stage

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: beefy12.nyi.freebsd.org/data/main-armv7-default/p772274a15b8b_s0630a06b2a/logs/cp2k-data-7.1.0.log Build URL: beefy12.nyi.freebsd.org/build.html?mastername=main-armv7-default&build=p772274a15b8b_s0630a06b2a Log: =>> Building science/cp2k-data build started at Sun Dec 19…

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CP2K/SIRIUS magnetic moment

Dear CP2K community, I would like to use SIRIUS library as a backend for CP2K to do spin-polarised calculations. As I am new to SIRIUS, I first took single Au atom (which has an odd number of electrons so it should exhibit some magnetic moment). I would like to force…

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Cp2k Xeon Benchmarks – OpenBenchmarking.org

1 Kernel Notes: Transparent Huge Pages: madviseProcessor Notes: Scaling Governor: intel_pstate powersave – CPU Microcode: 0xde – Thermald 2.3Security Notes: itlb_multihit: KVM: Mitigation of VMX disabled + l1tf: Not affected + mds: Not affected + meltdown: Not affected + spec_store_bypass: Mitigation of SSB disabled via prctl and seccomp + spectre_v1:…

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Orthonormality of MOs in K-point calculations

Hi it exactly means what is written. The orthogonality of the orbitals is not tested in k-point calculations. However, they are orthogonal by construction, unless there is a major problem in the calculation. regards Juerg Hutter ————————————————————– Juerg Hutter Phone : ++41 44 635 4491 Institut für Chemie E-mail: hut…@chem.uzh.ch Universität Zürich Winterthurerstrasse 190 CH-8057 Zürich,…

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main-armv6-default][science/cp2k-data] Failed for cp2k-data-7.1.0 in stage

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: beefy8.nyi.freebsd.org/data/main-armv6-default/pebf5105f9a4d_s23024f004a/logs/cp2k-data-7.1.0.log Build URL: beefy8.nyi.freebsd.org/build.html?mastername=main-armv6-default&build=pebf5105f9a4d_s23024f004a Log: =>> Building science/cp2k-data build started at Fri Oct 29…

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Is that possbile to use orbital free DFT code to to drive ab initio MD in CP2K?

Hi there is a OF method in CP2K (DFT/QS/METHOD OFGPW). However, this has never been used for production and is not actively developed. It certainly misses many options from state-of-the-art implementations. If you just want to use CP2K as a MD driver for an external program, it will be easier to use i-Pi or ASE. …

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Barostat cp2k error

Barostat cp2k error 08-10-2021 right! like your idea. suggest error barostat cp2k attentively would read, but has CP2K or with plane-wave-based codes such as Error. Espresso. In doing so, the Rahman barostat The statistical…

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Error in compiling cp2k 8.1

Dear all, I used the toolchain to set the environment, and the result (attached as toolchain.log) looks fine. Errors appear when compiling cp2k-8.1 with intel 18.0.5. Here is part of them extracted from the make.log (attached): cmp: CP2K/cp2k-8.1_t0608/cp2k-8.1/obj/git-ref: No such file or directory cp2k-8.1/src/grid/ref/grid_ref_task_list.c(446): error #3656: variable “old_transpose” may be…

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Accepted cp2k 8.2-1 (source) into experimental

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Sat, 02 Oct 2021 11:17:59 +0200 Source: cp2k Architecture: source Version: 8.2-1 Distribution: experimental Urgency: medium Maintainer: Debichem Team <debichem-de…@lists.alioth.debian.org> Changed-By: Michael Banck <mba…@debian.org> Changes: cp2k (8.2-1) experimental; urgency=medium . * New upstream point release. * debian/control (Build-Depends): Bump libxc-dev version…

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missing variable in OpenMP clause?

I’m trying to compile the CP2K trunk (revision 12663) with the Intel compiler and OpenMP. I get an error error #6752: Since the OpenMP* DEFAULT(NONE) clause applies, the PRIVATE, SHARED, REDUCTION, FIRSTPRIVATE, or LASTPRIVATE attribute must be explicitly specified for every variable.   [CNT]  in the file pw_methods.F. There are 3 offending…

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Raman spectra with cp2k – details of output files

Hello everyone,  Since I intend to calculate the Raman spectra using AIMD, I followed the tutorial on the cp2k website which uses the .cube files from cp2k and the Travis software for calculating the Raman spectra.  However, after calculating the raman spectra, I get different spectra files:1) spectrum_raman_aniso_ct_ 2) spectrum_raman_depol_ratio_ct_ 3) spectrum_raman_iso_ct_ 4) spectrum_raman_ortho_ct_…

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Calculating band gap in CP2K

Hi, I am trying to calculate band gap in CP2K for an electrolyte. On the internet, I found two ways to find the band gap. i) Look into one of the .pdos files generated by CP2K and find the energies where the occupation number changes from 2 to 0. Subtract…

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SCF calculation can not converge

Dear CP2K community,       I am a new CP2K’s user and recently started to CP2K for calculating a periodic system, like alloy slab. I need to run a geometry optimization, (before this opt step , I had tried use same structure without vacuum ,it can be converged )but…

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Problem of calculating melt structure with cp2k ab initio calculation method

At present, based on the ab initio calculation of the cp2k running silicate melt structure, the atoms in the initial structure are randomly distributed, and there are a total of 266 atoms. Through the xyz file, it is found that the system continues to expand during the running process, and…

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MXene TI2CO2 monolayer GEO_OPT gets stuck

Hello All, I created a Ti2CO2 monolayer (MXene)  that I will attach as an xyz file. I want to run GEO_OPT on this structure with periodic boundary conditions only in the XY directions. In my output RESULTS file  the first SCF converges in 106 steps, but then the file is…

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My symmetry-equivalent sites don’t have the same energy

Hello! Help, my symmetry-equivalent sites don’t have the same energy! __The problem:__ My system is insulating and antiferromagnetic Cr2O3 with a positive interstitial H in a hexagonal supercell. There are 6 equivalent* sites in a ‘doughnut’ around a large interstitial region. When I compute the total energy of these sites…

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CP2K: An electronic structure and molecular dynamics software package -Quickstep: Efficient and accurate electronic structure calculations

Abstract CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It is especially aimed at massively parallel and linear-scaling electronic structure methods and state-of-theart ab initio molecular dynamics simulations. Excellent performance for electronic structure calculations is…

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Plot of Electron Density Difference

Dear CP2K Users, I am currently learning how to make a plot of electron density difference for a system containing a molecule adsorbed on slabs. In order to do this, I have to first obtain cube files that have information on electron density. Since it is my first…

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cp2k9 under cygwin: bomd at graphite: slow?

Good day/good evening everybody: recently I compiled cp2k version 9 under Cygwin,and I am using it with BOMD to try predicting possible favourable orientations of small aromatic molecules next to graphite. I attach here one of trial examples, where a small aromatic moleculeis overwhelmed by the original slightly unfavourable initial…

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Industry Trends, Growth, Size, Segmentation, Future Demands, Latest Innovation, Sales Revenue by Regional Forecast

The latest research report on Molecular Dynamics Software market meticulously explains the key factors influencing the industry performance over 2021-2026, so as to help stakeholders gain a competitive edge. Further, it validates the forecasts mentioned through statistical data and proven research methodologies. Besides, the document offers recommendations to assist firms…

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The bulk modulus of diamond calculated by LAMMPS and CP2K(MM) is very different

Dear All, Firstly, I calculated bulk modulus of diamond by cp2k with QS METHOD, the lattice constant varied from 3.537 to 3.607, then the bulk modulus was calculated to 434.85 GPa by fitting the correlation between volume and energy (Birch–Murnaghan equation of state). And the result matches the real experiment.  Then, I calculated bulk modulus of diamond…

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cp2k cannot exit from queue when calculates large system being interfaced with ASE

Dear cp2k users and experts, I want to use ASE as a job submission tool on supercomputer and further I plan to use ASE to perform Genetic Algorithm global optimization. However, I find for relatively large system containing more than 200 atoms (generated by GA, so it is always a…

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