11

That is a modification of the standard XYZ file format and is called extended XYZ format, and not all programs are compatible with it. From the VMD Molfile Plugin Documentation page, it looks that VMD is only compatible with standard XYZ format. Also, take a look at this answer (to another question) about adding PBC info in VMD after loading standard XYZ ...


10

I am the person who package Avogadro2 as Flatpak. Stumble upon this thread randomly. I was not aware about this issue when I just randomly clicking on things. Not Avogadro power user, just software packager. Anyway, we are looking into that, but will probably take some time, since there is no detail error for us to work with at the moment. I suspect that ...


9

I was able to find a workaround to get open source PyMol installed on Windows. Christoph Gohlke at the University of California has a large library of precompiled Python wheel files of various scientific packages, including PyMol. I was able to find a Windows version for Python 3.8 pymol‑2.5.0a0‑cp38‑cp38‑win_amd64.whl and after downloading this file, I was ...


9

If you're using Linux its better if you install such packages using the apt-get method. apt-get install pymol I've encountered a similar error while installing MatPlotLib through conda. For more info you can follow this link: https://pymolwiki.org/index.php/Linux_Install Hope this helps :)


9

I am the author of Chemcraft. Your job contains a 2-dimensional PES scan, and currently Chemcraft can visualize only 1-dimensional scans. I plan to implement support of 2d scans in future. It is unclear for me (please give me some advice), in what form should these scans be visualized: colored map, or 3-d surface which can be rotated, or simply the ...


8

The following code should create a Cu surface and sort it by z index. We do this by providing tags for the positions of the atoms. [:, 2] allows us to select the z position of all atoms. from ase.build import bulk, surface from ase.build.tools import sort Cu = ase.build.bulk('Cu', 'fcc', a=3.6, cubic=True) surface = ase.build.surface(Cu, (1,1,1), 4, ...


8

Thanks to Tyberius for pointing out one issue in the database in their comment. The pycalphad database parser is strict, but also tries to prevent ambiguities or mistakes. I made the following corrections: Changed ELEMENT Y HCP_A3 8.89059+01 5.9664E+03 4.4434E+01 ! to ELEMENT Y HCP_A3 8.89059E+01 5.9664E+03 4.4434E+01 (adding E to the exponent of the mass) ...


8

This requires an additional IOP to do. It seems that Gaussian sets a separate lower and upper bound on the number of optimization steps that will be performed based on the number of coordinates and opt(maxcycle=N) can only set the max value within this range, but not any higher. IOP(1/152=N) changes this internal max value, allowing maxcycle to be raised as ...


7

Roughly speaking, absorption spectra are obtained by TDDFT calculations on optimized ground-state geometries, while emission spectra are obtained by TDDFT calculations on optimized excited state geometries. These are the results of the Franck-Condon approximation, which says that there is a high probability that a molecule is near its equilibrium geometry, ...


7

Please, check the version of OpenBabel you are using. At least, version 3.1.0 has the pdbqt format implemented: # obabel -v No input file or format spec or possibly a misplaced option. Most options must come after the input files. (-i -o -O -m can be anywhwere.) Open Babel 3.1.0 -- Jan 11 2021 -- 11:51:22 and: # obabel -L formats abinit -- ABINIT Output ...


7

The community wiki by Tyberius is a bit misleading here, you are not doing molecular dynamics calculations (IBRION=0) but likely a geometry optimization (IBRION=1,2,3). In the case of geometry optimization, the CHGCAR is not the predicted charge density, but is instead the charge density of the last completed step. For this reason, you should find no ...


6

The problem in the sript I had written was that my system was not able to handle that many variables at one go. So I made the calculations piecewise i.e. 40 atoms at a time and the results closely match the values one gets from the inbuilt function. In any case, calculating RMSF for just the C alpha atoms gives more information about the structural changes ...


6

All files are always created in the run directory where ORCA runs. I specifically did not want to deal with environment variables and path names and all that. Hope that helps! best wishes, Frank Neese


6

Camps is correct, VMD cannot directly parse the comment line of an xyz file because the extended ASE format is not recognized. You can, however, use a tcl-script to load the file and parse the comment line yourself. I am no tcl expert but here is an example that works for me: set filename [lindex $argv 0] # load the coordinates into vmd mol new $...


6

You likely need to ensure the correct anaconda environment is loaded. Use the following to get a 2.7 environment. conda create --name py2 python=2.7 conda activate 2.7 pip install ase==3.12.0 Your problems probably stem from issues with pip or the location of the installation. Use this method to ensure you have your 2.7 environment and you have ase in it. ...


6

In your comment, you mentioned that you may be testing many alloys (100,000s). I will assume that interested in taking more of a screening approach, rather than specifying precisely 100,000 alloys compositions. In that case, it is easy and faster to let pycalphad broadcast the conditions for you. It will skip any conditions that have independent mole ...


5

This is a weird quirk of the Gaussian input and I am unsure why it is implemented this way. The maxstep is given in a unit of 0.01 Bohr and it is presumed you do not wish to use a maxstep of less than 0.01 Bohr as this corresponds to about 0.005 angstroms. While I think this is a weird limitation to exist, you may consider that this is such a small distance ...


5

After some experimentation, I was able to track down the problem. Your output files tell me that you are using Gaussian 16. Upon inspection, the formchk utility in that version seems to put an "Internal Force Constants" section into the formatted checkpoint file in addition to the "Cartesian Force Constants" that VEDA is expecting. Thus, ...


5

Thanks to the generous time and comments of @ShoubhikRMaiti, I was able to recreate the simulation. The problem in my code was 2-fold: I was using the topology filed created by LigParGen, which had different charges on the C and H atoms in my simulation as in the paper. I did not think to check LigParGen's output, and that is my own fault. Also, I was using ...


5

This is not a full answer, because it does not solve the problem. But I hope to shed some light on why you are not getting the correct frequencies. Short answer: I suspect there is a bug in GAMESS Long answer: First of all I would advise you to go through the manual of GAMESS. There are lots of problems in the input file, and most of them can be easily ...


5

I can see two major problems: CCD != CC2 and I'm not certain if CC2 is available in GAMESS. CC2 is an approximation of CCSD, which is available in GAMESS. You may be able to use this since $\ce{NH3}$ is a fairly small molecule, though I don't know how time consuming this will be relative to your initial CCD calculation. TZV != TZVPP. The def2-TZVPP basis ...


5

Here are a few things you could try: ./configure --with-hdf5-libs=<options> --with-hdf5-include=<path> (note the double dashes) export HDF5_LIBS='-L/path/to/your/lib -lhdf5 -lhdf5fortran' before you ./configure Use the new cmake route to install QE (see example instructions here) which should be more robust and will likely replace the configure ...


5

I don't know any VASP-specific details, but the basic answer is that the three versions are almost identical, and solve the same equations in the same way. If we take vasp_std as the reference, then the differences are: vasp_gam If your system has time-reversal symmetry (true for most simulations), then $+k$ and $-k$ are symmetry-related and we can restrict ...


5

In the passage just above what you quoted, it says: For dynamic simulation (IBRION=0), the charge density on the file is the predicted charge density for the next step: i.e. it is compatible with the CONTCAR file, but incompatible with the last positions in the OUTCAR file. This means while the density in the CHGCAR file is a density for the position given ...


4

I think your problem was solved in this pull request. It is not merged yet because it breaks backward compatibility with python3.6 and lower. But if you use 3.7 or higher, you may try to install from that PR, and it should work. If it does not, please report the problem in the comments to that pull request. You can also ask questions related to the Bandup ...


4

From looking at the very long wavelength you specified, I assume your intent is to apply a static field to the calculation? I read here that EFIELD is intended for applying laser pulses and that you should use EXTERNAL_POTENTIAL instead, with the READ_FROM_CUBE option. Not sure whether printing the imposed potential is possible, but you could print the ...


4

It looks like Quantum Espresso is available through conda-forge which will be helpful. Conda Forge has worked to migrate many packages to osx-arm64 and will rebuild packages for you. The easy way is to update the list of packages to migrate as a pull-request. Assuming that goes through, various scripts will update the qe package on conda-forge and you'll get ...


4

# # To run VASP this script calls $vasp_std # (or posibly $vasp_gam and/or $vasp_ncl). # These variables can be defined by sourcing vaspcmd . vaspcmd 2> /dev/null As mentioned in the comments, the answer is actually in your question. vaspcmd is just any script you provide that defines the $vasp_std, $vasp_gam and $vasp_ncl variables which give the full ...


4

If by "standard", you mean an "official" VASP-supported program, then the answer is no. VASP gives you the raw text output for you to deal with on your own. That being said, the vasprun.xml file produced at the end of a run contains many of the important calculation results, so any parser than can read an XML file can also parse this data ...


4

I could be wrong, but I am fairly certain that line of the CONTCAR technically doesn't matter. If you put a O instead of H, but put the potentials in the right order, you will get the right result even though the element is wrong. For visualization, it will definitely be wrong but I don't think the calculated result is wrong. In tools such as ASE the ...


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