91
Simulation algorithms and theory / Re: GCMC combination with NpT-MD
« Last post by aemelianova on March 26, 2019, 03:22:00 PM »Thank you very much for the answer.
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92
Simulation algorithms and theory / Re: GCMC combination with NpT-MD
« Last post by David Dubbeldam on March 23, 2019, 06:26:22 PM »That move can be simulated with a NVE hybrid-move combined with a volume move.
There is trial-attempt on implementing some NPH-like move with
HybridNPHMoveProbability 0.05
but that is untested and you will have to look at the code whether that actually works and the acceptance rule is correct and modify it if need be.
There is trial-attempt on implementing some NPH-like move with
HybridNPHMoveProbability 0.05
but that is untested and you will have to look at the code whether that actually works and the acceptance rule is correct and modify it if need be.
93
Simulation algorithms and theory / GCMC combination with NpT-MD
« Last post by aemelianova on March 15, 2019, 08:52:50 PM »Dear Prof. Dubbeldam,
RASPA documentation shows how to perform hybrid MD/MC simulation by a combination GCMC with short NVE MD-run.
Is there any way to set up a combination of GCMC and short MD-run in NpT ensemble (instead of NVT) in RASPA?
Thank you,
Alina
RASPA documentation shows how to perform hybrid MD/MC simulation by a combination GCMC with short NVE MD-run.
Is there any way to set up a combination of GCMC and short MD-run in NpT ensemble (instead of NVT) in RASPA?
Thank you,
Alina
94
Output files / Re: ENERGY DRIFT
« Last post by David Dubbeldam on March 06, 2019, 02:29:19 PM »This can possibly occur when not all potentials are well-defined. An example is when the hydrogens do NOT have a Lennard-Jones potential, but the connecting atom has a VDW radius that encompasses the hydrogen (or it should). But if the VDW radius is too small, then at high density the atoms will start to overlap leading to numerical problems.
95
Output files / Re: ENERGY DRIFT
« Last post by Somananda Sanyal on March 04, 2019, 01:49:48 PM »Dear Dr. Dubbeldam,
I am getting the same error with the latest version of RASPA, i.e. 2.0.35.
How to resolve the warning and if I may know too why is it occurring?
Thanks.
Somananda
I am getting the same error with the latest version of RASPA, i.e. 2.0.35.
How to resolve the warning and if I may know too why is it occurring?
Thanks.
Somananda
96
Input files and parameters / Re: ChargeFromChargeEquilibration
« Last post by David Dubbeldam on January 28, 2019, 07:57:40 PM »Check the format of the CIF file and compare it to the other ones to see where it goes wrong.
Usually, the error is printed to the console about what goes wrong with the reading.
Usually, the error is printed to the console about what goes wrong with the reading.
97
General / Re: Parallelization of RASPA simulations with Golem
« Last post by nowakoww on January 25, 2019, 03:59:37 PM »Hello,
It's Golem here. As mentioned in the post above, we have prepared a thin client. It hides all the complexity of Golem from RASPA users as much as possible. There's no need to install Golem on your computer. Now, you only have to install the thin client, provide connectivity details and run the example RASPA calculations provided within the installation pack to test the installation.
The thin client doesn't contain any Golem-specific components. It just sends computing tasks along with input data to a remote server that acts as a Golem requestor node. Currently this requestor node is hosted on AWS and managed by the Golem Team. The requestor node knows how to speak to the Golem network using the Golem protocol in order to find provider nodes which will actually do computational work in parallel. The more provider nodes there are in the Golem network, the better parallelization we can achieve and obtain results faster.
In the installation pack there are two main directories:
\golemrpc - contains thin client code,
\examples - contains example python script raspa_remote.py and \examples\cifs subfolder with input data.
We've tried to ensure that the code is well documented. To get familiar whit the thin client and the example, please read comments in the code. Also, don't hesitate to contact us either on this forum or via email or any other communication channel we use (see https://golem.network/).
How the example works
raspa_remote.py reads input .cif files and instructs remote requestor node to create computation tasks (one task per one input file) in the Golem network which can be then executed by provider nodes. The provided example runs get_helium_void_fraction() for two selected .cif files from \examples\cifs. After completing the calculations the results for each task are saved in \examples\cifs\<task_id>-output folder, e.g. \examples\cifs\40e0d906-20aa-11e9-8e1c-c772b47c74b3-output.
You can, of course, modify the example to perform your own RASPA calculations on your own input data.
The nature of the Golem network enables performing calculations of parallel tasks on virtually unlimited number of nodes (depending on how many independent subtasks your entire computational task can be divided). However, for the purpose of testing the RASPA thin client we have setup a test environment consisting of just several provider nodes. This means that you can perform calculations on several input files in parallel.
How to install the client and run the example?
The installation is very straightforward. Please follow the instructions here: https://github.com/golemfactory/golemrpc
Note that the thin client connects with the remote Golem requestor node on AWS. To enable secure connection you need credential files: 'golemcli_aws.tck' and 'rpc_cert_aws.pem'. To obtain those files, please contact michal.plebanski@golem.network or wiktor.nowakowski@golem.network.
We would much appreciate your feedback about using the thin client. We would also appreciate if you spend a small quantum of time to answear our questions from the post above. We are open to any discussions on any time.
Best regards,
Wiktor
It's Golem here. As mentioned in the post above, we have prepared a thin client. It hides all the complexity of Golem from RASPA users as much as possible. There's no need to install Golem on your computer. Now, you only have to install the thin client, provide connectivity details and run the example RASPA calculations provided within the installation pack to test the installation.
The thin client doesn't contain any Golem-specific components. It just sends computing tasks along with input data to a remote server that acts as a Golem requestor node. Currently this requestor node is hosted on AWS and managed by the Golem Team. The requestor node knows how to speak to the Golem network using the Golem protocol in order to find provider nodes which will actually do computational work in parallel. The more provider nodes there are in the Golem network, the better parallelization we can achieve and obtain results faster.
In the installation pack there are two main directories:
\golemrpc - contains thin client code,
\examples - contains example python script raspa_remote.py and \examples\cifs subfolder with input data.
We've tried to ensure that the code is well documented. To get familiar whit the thin client and the example, please read comments in the code. Also, don't hesitate to contact us either on this forum or via email or any other communication channel we use (see https://golem.network/).
How the example works
raspa_remote.py reads input .cif files and instructs remote requestor node to create computation tasks (one task per one input file) in the Golem network which can be then executed by provider nodes. The provided example runs get_helium_void_fraction() for two selected .cif files from \examples\cifs. After completing the calculations the results for each task are saved in \examples\cifs\<task_id>-output folder, e.g. \examples\cifs\40e0d906-20aa-11e9-8e1c-c772b47c74b3-output.
You can, of course, modify the example to perform your own RASPA calculations on your own input data.
The nature of the Golem network enables performing calculations of parallel tasks on virtually unlimited number of nodes (depending on how many independent subtasks your entire computational task can be divided). However, for the purpose of testing the RASPA thin client we have setup a test environment consisting of just several provider nodes. This means that you can perform calculations on several input files in parallel.
How to install the client and run the example?
The installation is very straightforward. Please follow the instructions here: https://github.com/golemfactory/golemrpc
Note that the thin client connects with the remote Golem requestor node on AWS. To enable secure connection you need credential files: 'golemcli_aws.tck' and 'rpc_cert_aws.pem'. To obtain those files, please contact michal.plebanski@golem.network or wiktor.nowakowski@golem.network.
We would much appreciate your feedback about using the thin client. We would also appreciate if you spend a small quantum of time to answear our questions from the post above. We are open to any discussions on any time.
Best regards,
Wiktor
98
Input files and parameters / Re: (resolved)ChargeFromChargeEquilibration
« Last post by anne on January 21, 2019, 04:23:38 AM »Hi David;
I have a followed-up question of this ChargeFromChargeEquilibriateion. It worked when I tried on MIL-53, MIL-100-primitive files which were in the share/raspa/structure/cif folder. However, it didn't work on the MIL-100-Fe.cif file I downloaded from CCDC (Link https://www.ccdc.cam.ac.uk/structures/Search?Compound=MIL-100&DatabaseToSearch=Published). There is no output files/folders like Output, Movie, etc. after reading the cif file and force-field files. Here is the simulation.input file. I also attached the MIL-100-Fe.cif file.
SimulationType MC
NumberOfCycles 0
NumberOfInitializationCycles 0
PrintEvery 100
RestartFile no
Forcefield local
ChargeMethod Coulomb
CutOff 12.0
ChargeFromChargeEquilibration yes
ChargeEquilibrationPeriodic yes
ChargeEquilibrationEwald yes
SymmetrizeFrameworkCharges no
Framework 0
FrameworkName MIL-100-Fe
UnitCells 1 1 1
ExternalTemperature 298.0
ExternalPressure 0.0
InputFileType cif
I am sure that the simulation.input file should be good and wondering if this is because there are no hydrogen atoms in the downloaded MIL-100-Fe.cif files (please see the attachment).
I appreciate it in advance.
Anne
I have a followed-up question of this ChargeFromChargeEquilibriateion. It worked when I tried on MIL-53, MIL-100-primitive files which were in the share/raspa/structure/cif folder. However, it didn't work on the MIL-100-Fe.cif file I downloaded from CCDC (Link https://www.ccdc.cam.ac.uk/structures/Search?Compound=MIL-100&DatabaseToSearch=Published). There is no output files/folders like Output, Movie, etc. after reading the cif file and force-field files. Here is the simulation.input file. I also attached the MIL-100-Fe.cif file.
SimulationType MC
NumberOfCycles 0
NumberOfInitializationCycles 0
PrintEvery 100
RestartFile no
Forcefield local
ChargeMethod Coulomb
CutOff 12.0
ChargeFromChargeEquilibration yes
ChargeEquilibrationPeriodic yes
ChargeEquilibrationEwald yes
SymmetrizeFrameworkCharges no
Framework 0
FrameworkName MIL-100-Fe
UnitCells 1 1 1
ExternalTemperature 298.0
ExternalPressure 0.0
InputFileType cif
I am sure that the simulation.input file should be good and wondering if this is because there are no hydrogen atoms in the downloaded MIL-100-Fe.cif files (please see the attachment).
I appreciate it in advance.
Anne
99
Input files and parameters / Re: Single Point Energy Calculation?
« Last post by David Dubbeldam on January 17, 2019, 04:58:36 PM »A single point is run by just using 0 cycles. To read in a configuration you can use the Restart-file (see manual).
A quick way of creating that file is to use 0 cycles and create a single molecule. That will write out the Restart-file containing (some) atomic positions of the molecule.
You can then edit this file, read it in, and run for 0 cycles to compute a 'single point' energy.
A quick way of creating that file is to use 0 cycles and create a single molecule. That will write out the Restart-file containing (some) atomic positions of the molecule.
You can then edit this file, read it in, and run for 0 cycles to compute a 'single point' energy.
100
Input files and parameters / Single Point Energy Calculation?
« Last post by sen on January 15, 2019, 11:00:16 PM »Hi all,
I'm a new user in raspa. Is it possible to for raspa to read in a configuration file that contains the MOF and one adsorbate coordinate, and then do a single point energy calculation? What I want is the energy of this system calculated from force filed.
Thanks!
I'm a new user in raspa. Is it possible to for raspa to read in a configuration file that contains the MOF and one adsorbate coordinate, and then do a single point energy calculation? What I want is the energy of this system calculated from force filed.
Thanks!