Questions tagged [cp2k]
For questions about (or related to) the software CP2K.
30
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Normal coordinate analysis in TRAVIS
I have run a few AIMD calculations of some impurities trapped in a solid using CP2K and TRAVIS to simulate the resulting infrared spectrum. While the infrared spectrum was simulated well, there is no ...
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Is memory per core more import than # of memory channels for high performance VASP calculation?
Cross posted on StackOverflow.
I ask this question cause recently my department want to purchase a HPC cluster mainly for first principle calculation. For now we have three choices:
(1) Per node dual ...
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1
answer
106
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Can CP2K be used for slab calculations?
I am trying to map out potential energy of a slab surface + cation interaction, since VASP has been giving me very not-so-reliable results I wanted to know if CP2K have the ability to do such ...
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0
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How to calculate constraint force for angle constraint in CP2K NVT MD simulation?
I am running a CP2K NVT molecular dynamics simulation and want to apply an angle constraint between three atoms. In my previous simulations, I used a bond constraint between two atoms, and it was easy ...
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Getting CP2K to print the COLVAR info
Is it possible to make CP2K to print the values of all the defined COLVARs? I did find the following subsection in COLVAR section
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1
answer
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Model coordination complex using GROMACS or CP2K
Is it possible to compute a 3D model of a calcium EDTA complex and it's energy? If so, how should I go about doing it or where can I obtain relevant information regarding computation methods?
I ...
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1
answer
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SCF energy keeps on fluctuating between two values, instead of converging, why?
Sometimes I have observed this phenomenon where my calculations' SCF iterations keep on fluctuating between two values, and not converging. I have observed it in all sort of systems, ranging from ...
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1
answer
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Ab-initio molecular dynamics of liquid systems: best tools and resources
I have been studying liquid systems (particularly deep eutectic solvents) using classical molecular dynamics (MD) simulations. The main drawback of classical MD is the arbitrariness of the potential ...
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CP2K geometry optimization SCF takes 3000s for a step [closed]
I am new to CP2K and doing a geometry optimization for a cluster. At the beginning everything looks good, each SCF step takes about 13 seconds, the energy drops quickly and the convergence looks like ...
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8
votes
1
answer
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Total force calculated with cp2k not zero
I performed DFT calculations for a box of 64 water molecules under Periodic Boundary Condition using CP2K. I found that the forces on each atom do not sum up to zero, as shown in the attached figure. ...
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7
votes
3
answers
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Calculate Hessian for configurations that are not at the minimum of the Potential Energy Surface
I want to calculate the Hessian matrix for molecular configurations that are not at the minimum of the Potential Energy Surface, using cp2k. But it seems that cp2k requires the configuration to be ...
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8
votes
1
answer
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How to run 2nd generation CPMD in CP2K?
I believe CP2K by default implements Born–Oppenheimer MD. I have seen many recent papers that use 2nd generation Car–Parrinello MD using CP2K. But I couldn't find any direct way of switching to 2nd-...
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answers
384
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Setup for 4-point flexible water model [closed]
I tried to search online if there are examples or suggestions on how to set up a 4-point flexible water model, such as TIP4P/2005f, qTIP4P/f, TIP4P/$\epsilon$ FLEX, etc., but there's no clear example ...
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Molecular dynamics to reproduce dispersion interactions [closed]
I'm trying to simulate the behavior of chromophore molecules incorporated into a polymer under an external electric field.
I've tried to use classical molecular dynamics (GROMACS) but it's unable to ...
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9
votes
1
answer
305
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What is a "charged system" in this specific context?
I'm doing a polarization calculation for the first time. To specify one of the input parameters (the "reference point") correctly, I have to figure out if my system is "charged." ...
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Kinetic energy cut-off for Gaussian-type orbitals when applying periodic boundary conditions [duplicate]
I have a solid with PBC (periodic boundary conditions) and I want to perform a DFT simulation. I use GTO as the basis. In a paper I read, I can transform the GTO to a Bloch function (crystalline ...
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10
votes
1
answer
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Reading complex potential into CP2K
Is it possible to read a complex potential into CP2K? I have generated a potential using FDTD at a given frequency, which results in a complex result. The potential is to be read in to a real time ...
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CP2K Spherical Cell [closed]
I'm trying to run a gas phase cluster calculation in CP2K. I want to create an outside force to constrain water molecules that are in the simulation within a radius of a central ion. I want to create ...
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7
votes
1
answer
577
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cp2k conserved quantity changed when restart NVT MD?
The details are descripted elsewhere, but got no answer for days, so I post it here for help.
As title said, I noticed a relatively big change in conserved quantity and don't know why.
I've upload ...
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14
votes
1
answer
285
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Is basis set superposition error reduced when using the GAPW method?
CP2K implements the Gaussian and Augmented Planewaves (GAPW) approach for all-electron calculations. My understanding is that the GAPW method involves using atom-centered Gaussian type orbitals to ...
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answers
147
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Periodic polarizable QM/MM embedding [closed]
Are there any standalone open source software codes available for periodic polarizable QM/MM embedding MD simulations? In my knowledge, CP2K only has the option for electrostatic embedding and other ...
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8
votes
1
answer
567
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Failure of CP2K density functional software to converge for a 64 Si atom amorphous structure
The structure was created using Stillinger Weber with LAMMPS.
The command I used was the following:
...
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15
votes
0
answers
263
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CP2K vs BigDFT comparison [closed]
I typically run DFT calculations with 1000 to 5000 atoms using CP2K. This works fine but I'm interested in BigDFT also. Is there anyone here that has experience using BigDFT and is able to compare ...
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12
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1
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562
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Geometric optimization taking a long time. Are my convergence criteria too tight in CP2K?
I have been having trouble with the VIBRATIONAL_ANALYSIS routine. Namely, the routine keeps timing out. I am trying to find the vibrational modes of Pyridine in a non periodic system, as well as $\ce{...
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8
votes
1
answer
264
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Reading in E-field with CP2K
I have figured out a way to input a custom electric field in a .cube format, but I am not sure I am doing it in the proper way. Currently my file contains information for the magnitude of the electric ...
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7
votes
1
answer
188
views
What are the default units for the core hamiltonian and the density AO matrices in CP2K?
I have a few questions about default units. I am trying to find the default units for the density matrix and the core hamiltonian. I am assuming they are in e/(bohr)$^3$ and Hartrees respectively. I ...
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16
votes
1
answer
497
views
Is there any reason not to sum the kinetic and potential energy from an NPT simulation to get internal energy?
I would be very grateful for some newbie-level advice from a thermodynamics guru.
I ran NPT simulations on a particular system (in CP2K software) to get fluid densities for use in fluid dynamics ...
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10
votes
2
answers
282
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What are some methods for modeling bulk phase infrared spectra?
I am interested in predicting the infrared spectra of bulk phase molecules, it seems that AIMD (ab initio molecular dynamics) is the current best approach. I have found a tutorial on using CP2K to do ...
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8
votes
1
answer
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Is it possible to use the Parrinello-Rahman barostat for NPT simulations in CP2K?
It is possible to use different types of thermostats in CP2K by specifying them in the corresponding section of the input as mentioned here. But there is no mention of specifying the barostat type in ...
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15
votes
2
answers
1k
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What exactly is the "Optimizer" in CP2K geometry optimization?
I'm just now starting to use the program CP2K, and I am having trouble understanding the difference between the optimizer options (CG, BFGS, LBFGS). I have seen ...
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