Recent Posts

Pages: 1 ... 8 9 [10]
91
General / Run RASPA using MPI
« Last post by manuelbenavent on July 17, 2020, 10:07:46 AM »
Dear developers,

I was wondering if I could run RASPA using MPI. Or is there any other way to make parallelization?

Thanks
Manuel
92
Input files and parameters / Re: 1_2_ethanediol TraPPE modell
« Last post by Christopher on July 16, 2020, 05:51:46 PM »
Maybe simulation.input would be interessting:

SimulationType                    MonteCarlo
NumberOfCycles                    50000
NumberOfInitializationCycles      50000
PrintEvery                        10
RestartFile                       no

CutOff                            14.0
CutOffVDW                         14.0
CutOffCoulomb                     14.0
EwaldPrecision                    1e-12
Forcefield                        local
WriteBinaryRestartFileEvery       1000
ContinueAfterCrash                no

Box 0
BoxLengths 40 40 40
BoxAngles 90 90 90
ExternalTemperature 600
ComputeMolecularPressure yes

Box 1
BoxLengths 40 40 40
BoxAngles 90 90 90
ExternalTemperature 600
ComputeMolecularPressure yes

GibbsVolumeChangeProbability 0.1

Component 0 MoleculeName                      1_2_ethanediol
            StartingBead                      0
            MoleculeDefinition                local
            Intra14ChargeChargeScalingValue   0.5
            Intra14VDWScalingValue            0
            TranslationProbability            1.0
            RandomTranslationProbability      1.0
            RotationProbability               1.0
            GibbsSwapProbability              1.0
            ReinsertionProbability            1.0
            CBMCProbability                   1.0
            CreateNumberOfMolecules           100 100


I varied EwaldPrecision from 1e-6 to 1e-12 and also other starting conditions like box lenghts or the number of molecules in a box. But everytime the simulation get's stuck.

Best Christopher
93
Input files and parameters / Re: 1_2_ethanediol TraPPE modell
« Last post by Christopher on July 16, 2020, 05:49:28 PM »
Dear Dr. Dubbeldam:
thanks for taking the time to help me!
I'm getting the same output. And also the forcefield in the output file looks fine. The version in the outputfile is
RASPA 2.0.38
Compiled as a 64-bits application
Compiler: gcc 7.4.1 20190905 [gcc-7-branch revision 275407]
Compile Date = Jul  1 2020, Compile Time = 13:22:41

I use this version of force_field_mixing_rules.def:
# general rule for shifted vs truncated
truncated
# general rule tailcorrections
yes
# number of defined interactions
13
# type interaction
He             LENNARD_JONES    10.9     2.64
CH4_sp3        LENNARD_JONES   148.0     3.73
CH3_sp3        LENNARD_JONES    98.0     3.75
CH2_sp3        LENNARD_JONES    46.0     3.95
CH_sp3         LENNARD_JONES    10.0     4.68
C_sp3          LENNARD_JONES     0.5     6.4
O_co2          LENNARD_JONES    79.0     3.05
C_co2          LENNARD_JONES    27.0     2.80
N_n2           LENNARD_JONES    36.0     3.31
O_alc          LENNARD_JONES    93.0     3.02
H_alc          LENNARD_JONES     0.0     0.0
CH2_alc        LENNARD_JONES    46.0     3.95
dummy          LENNARD_JONES     0.0     0.0
# general mixing rule for Lennard-Jones
Lorentz-Berthelot


And pseudo_atoms.def
#number of pseudo atoms
13
#type      print   as    chem  oxidation   mass        charge   polarization B-factor radii  connectivity anisotropic anisotropic-type   tinker-type
CH4_sp3    yes     C     C     0           16.04246    0.0      0.0          1.0      1.00   0            0           absolute           0
CH3_sp3    yes     C     C     0           15.03452    0.0      0.0          1.0      1.00   0            0           absolute           0
CH2_sp3    yes     C     C     0           14.02658    0.0      0.0          1.0      1.00   0            0           absolute           0
CH_sp3     yes     C     C     0           13.01864    0.0      0.0          1.0      1.00   0            0           absolute           0
C_sp3      yes     C     C     0           12.0        0.0      0.0          1.0      1.00   0            0           absolute           0
O_alc      yes     O     O     0           15.9994    -0.7      0.0          1.0      1.00   0            0           relative           0
H_alc      yes     H     H     0            1.00794    0.435    0.0          1.0      1.00   0            0           relative           0
CH2_alc    yes     C     C     0           14.02658    0.265    0.0          1.0      1.00   0            0           relative           0
C_co2      yes     C     C     0           12.0107     0.7      1.508        1.0      0.720  0            0           relative           0
O_co2      yes     O     O     0           15.9994    -0.35     0.9475       1.0      0.68   0            0           relative           0
N_n2       yes     N     N     0           14.00674   -0.482    0.0          1.0      0.7    0            0           relative           0
N_com      no      N     N     0           0.0         0.964    0.0          1.0      0.7    0            0           relative           0
dummy      no      N     N     0           0.0         0.0      0.0          1.0      1.00   0            0           relative           0

Have you ever tried TraPPE models of diols? I still can't figure out any reason, why it is not working.
If you have any hint, I would really appreciate!

Best
Christopher
94
Input files and parameters / Re: Defining new molecules for RASPA MC Calculation
« Last post by manuelbenavent on July 14, 2020, 10:47:07 PM »
Quote from: dubbelda on July 14, 2020, 12:48:35 PM
The positions are relative to each other. In the output file you can see that it reorients the molecule anyway (according to the matrix of inertia).

Dear Dubbelda

But is this ok for me to define the pyridine´s atoms in such a way?

Allow me another question. I want to prepare an MFI zeolite structure in a 1x1x2 with a single Al atom and a corresponding H as counterion. What is the best way for me to prepare such input? I´ve tried to open an MFI.cif file, build a 1x1x2 supercell, and adding both the Al and the H in Avogadro. But it seems that the way is written by Avogadro is not compatible with RASPA. Can you also provide some insight into this?

Thanks
Manuel
95
Input files and parameters / Re: pseudo_atom radii
« Last post by dubbelda on July 14, 2020, 12:57:09 PM »
The radii are used to compute bonding in flexible frameworks.
For small rigid molecules you define the relative positions of all atoms (including for example dummy atoms).
96
Input files and parameters / Re: Establishing water model and simulation pressure setup
« Last post by dubbelda on July 14, 2020, 12:55:30 PM »
Yes, when FugacityCoefficient is set to 1.0, then ExternalPressure is the fugacity which you input.
97
Input files and parameters / Re: Problem including anisotropic factors for isopropanol AUA4 forcefield
« Last post by dubbelda on July 14, 2020, 12:53:03 PM »
I have not used that in many, many years. I am not sure that is working properly. You could check the source code.
98
General / Re: net charge warning
« Last post by dubbelda on July 14, 2020, 12:51:32 PM »
Recheck how you use the charges, whether you use them from the 'pseudo_atoms.def' files or whether you use them directly from the CIF-file.

When you have negative excess adsorption, you crossed the vapor pressure according to the Peng-Robinson equation of state are inputted from the critical constants in the molecule file.
So either that is inaccurate, or your force field parameters of the molecule does not reproduces that vapor pressure.
99
Input files and parameters / Re: Defining new molecules for RASPA MC Calculation
« Last post by dubbelda on July 14, 2020, 12:48:35 PM »
The positions are relative to each other. In the output file you can see that it reorients the molecule anyway (according to the matrix of inertia).
100
Visualization / Re: create movie
« Last post by dubbelda on July 14, 2020, 12:46:08 PM »
With the current version of iRASPA for windows (1.1.18) you should be able to create movies (h265, h265, or vp9).
Pages: 1 ... 8 9 [10]