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How to convet cif file to cif file with P1symmetry #34

Open reshujose91 opened 6 years ago

reshujose91 commented 6 years ago

Hello all. I am a beginner to RASPA package. I tried running structure.cif file in python but its showing some error. So how I can convert it to P1 symmetry cif file as mentioned in the below link- https://github.com/numat/RASPA2/wiki/Workflow Since Material studio is not an open source, can somebody tell me another way? I am doing the calculation in linux using normal computer.

Thanks,

patrickfuller commented 6 years ago

Hi,

You can use an open-source library such as open babel to do this. Hope this helps!

remseven commented 6 years ago

Hello, Agovadro does that (Crystallography --> Spacegroup --> Set spacegroup), probably using Openbabel though. However I don't think that's your problem. I am using non P1 symmettry cif files in RASPA. A few month ago I was in your position and realized that the header of my cif files was different from the one already available in RASPA, in particular where the symmetry is defined. I recommend you check that, and adapt to what is already working in RASPA. You will also probably need to ensure that the spacegroup definition matches RASPA's. Check RASPA manual (or source code if needed), there are all listed. Cheers,

reshujose91 commented 6 years ago

Thanks a lot Fuller and Petuya for your kind reply. Can you please provide me an input file for getting the adsorption isotherm of MOF. I want to run it on sever. I could get a script file and input file from raspa manual but not sure about running it. I am attaching the same.. Can you please also tell me whether one input file sufficient or i need to put pseudo_atoms.def, force_field_mxing_rules.def',`force_field.def' and zframework.def files also in the input folder? I have no idea how to make .def files.. I need to only get an adsorption isotherm of the optimized geometry of my MOF by taking O2 and N2 and H2 as gases. Kindly check the files attached and please provide me an executable one if possible

Thanks a lot, Reshma

On Thu, Mar 22, 2018 at 8:15 PM, Rémi Pétuya notifications@github.com wrote:

Hello, Agovadro does that (Crystallography --> Spacegroup --> Set spacegroup). However I don't think that's your problem. I am using non P1 symmettry cif files in RASPA. A few month ago I was in your position and realized that the header of my cif files was different from the one already available in RASPA, in particular where the symmetry is defined. I recommend you check that, and adapt to what is already working in RASPA. You will also probably need to ensure that the spacegroup definition matches RASPA's. Check RASPA manual (or source code if needed), there are all listed. Cheers,

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/numat/RASPA2/issues/34#issuecomment-375332094, or mute the thread https://github.com/notifications/unsubscribe-auth/Aj6ICZUWvEaRJWoVllr4zH7OWDcgWRlHks5tg7kdgaJpZM4S2lsX .

reshujose91 commented 6 years ago

Dear All,

I am able to install the software in my system successfully and performed some trial calculations as well. Now I am trying to do some calculations using RASPA software to get the adsorption isotherm for a MOF with O2 gas. I am facing an error while inputting the CIF file of mine but the CIF given in software is working properly. Is there any other format with which I can input my structure other than .cif so that the software can red it (like .pdb, .xyz). Or will you please suggest me an open software to get the CIF file in the required format for RASPA software.

I also wanted to know whether I can get the adsorption isotherm for a range of pressure within an input file. Or I should take reading for a particular pressure and I have to plot all data manually? How you are basically obtaining the adsorption isotherm plot over a range of pressure as explained in the manual. Will you please help me in plotting the isotherm for a range of pressure from 0bar to 1bar. Thanking You,

Sincerely, Reshma Jose C/o Gopalan Rajaraman IIT Bombay

On Fri, Mar 23, 2018 at 9:05 AM, Reshma Jose reshma.iiserb@gmail.com wrote:

Thanks a lot Fuller and Petuya for your kind reply. Can you please provide me an input file for getting the adsorption isotherm of MOF. I want to run it on sever. I could get a script file and input file from raspa manual but not sure about running it. I am attaching the same.. Can you please also tell me whether one input file sufficient or i need to put pseudo_atoms.def, force_field_mxing_rules.def',`force_field.def' and zframework.def files also in the input folder? I have no idea how to make .def files.. I need to only get an adsorption isotherm of the optimized geometry of my MOF by taking O2 and N2 and H2 as gases. Kindly check the files attached and please provide me an executable one if possible

Thanks a lot, Reshma

On Thu, Mar 22, 2018 at 8:15 PM, Rémi Pétuya notifications@github.com wrote:

Hello, Agovadro does that (Crystallography --> Spacegroup --> Set spacegroup). However I don't think that's your problem. I am using non P1 symmettry cif files in RASPA. A few month ago I was in your position and realized that the header of my cif files was different from the one already available in RASPA, in particular where the symmetry is defined. I recommend you check that, and adapt to what is already working in RASPA. You will also probably need to ensure that the spacegroup definition matches RASPA's. Check RASPA manual (or source code if needed), there are all listed. Cheers,

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/numat/RASPA2/issues/34#issuecomment-375332094, or mute the thread https://github.com/notifications/unsubscribe-auth/Aj6ICZUWvEaRJWoVllr4zH7OWDcgWRlHks5tg7kdgaJpZM4S2lsX .

reshujose91 commented 6 years ago

Dear all, Can anyone kindly tell me how to plot the adsorption isotherm for O2 gas onto MOF. I have taken readings for different pressures and tried tried plotting manually. But I am not able to get a saturation point in my plot rather the plot is going as a straight line. Should I need to take the output data of initial pressure and with that file I should look for the next step of adsorption? Can anyone please help me in this regards,

Thanks,

On Thu, Apr 19, 2018 at 8:35 AM, Reshma Jose reshma.iiserb@gmail.com wrote:

Dear All,

I am able to install the software in my system successfully and performed some trial calculations as well. Now I am trying to do some calculations using RASPA software to get the adsorption isotherm for a MOF with O2 gas. I am facing an error while inputting the CIF file of mine but the CIF given in software is working properly. Is there any other format with which I can input my structure other than .cif so that the software can red it (like .pdb, .xyz). Or will you please suggest me an open software to get the CIF file in the required format for RASPA software.

I also wanted to know whether I can get the adsorption isotherm for a range of pressure within an input file. Or I should take reading for a particular pressure and I have to plot all data manually? How you are basically obtaining the adsorption isotherm plot over a range of pressure as explained in the manual. Will you please help me in plotting the isotherm for a range of pressure from 0bar to 1bar. Thanking You,

Sincerely, Reshma Jose C/o Gopalan Rajaraman IIT Bombay

On Fri, Mar 23, 2018 at 9:05 AM, Reshma Jose reshma.iiserb@gmail.com wrote:

Thanks a lot Fuller and Petuya for your kind reply. Can you please provide me an input file for getting the adsorption isotherm of MOF. I want to run it on sever. I could get a script file and input file from raspa manual but not sure about running it. I am attaching the same.. Can you please also tell me whether one input file sufficient or i need to put pseudo_atoms.def, force_field_mxing_rules.def',`force_field.def' and zframework.def files also in the input folder? I have no idea how to make .def files.. I need to only get an adsorption isotherm of the optimized geometry of my MOF by taking O2 and N2 and H2 as gases. Kindly check the files attached and please provide me an executable one if possible

Thanks a lot, Reshma

On Thu, Mar 22, 2018 at 8:15 PM, Rémi Pétuya notifications@github.com wrote:

Hello, Agovadro does that (Crystallography --> Spacegroup --> Set spacegroup). However I don't think that's your problem. I am using non P1 symmettry cif files in RASPA. A few month ago I was in your position and realized that the header of my cif files was different from the one already available in RASPA, in particular where the symmetry is defined. I recommend you check that, and adapt to what is already working in RASPA. You will also probably need to ensure that the spacegroup definition matches RASPA's. Check RASPA manual (or source code if needed), there are all listed. Cheers,

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/numat/RASPA2/issues/34#issuecomment-375332094, or mute the thread https://github.com/notifications/unsubscribe-auth/Aj6ICZUWvEaRJWoVllr4zH7OWDcgWRlHks5tg7kdgaJpZM4S2lsX .

somanandasanyal commented 5 years ago

Dear All, 

    I am also an absolute beginner in RASPA and facing the similar problems like Reshma.

Could you solve the problem with cif files? I am working with a Zn-MOF and it has Pbcn space group. While trying to calculate the Helium void for the starting calculation, I am getting an error: ERROR in cif-file: no proper space group definition found Can anyone help in solving this problem? May I get an input file as an example? Thanks in advance.

Regards, Somananda