News:

SMF - Just Installed!

Main Menu
Menu

Show posts

This section allows you to view all posts made by this member. Note that you can only see posts made in areas you currently have access to.

Show posts Menu

Topics - Mozhdeh

#1
Dear Pro. Dubbledam

I have encounter a message from program as:


Realloc MaxNumberOfCoulombicSites: 4672
Realloc MaxNumberOfCoulombicSites: 5184

I lookup in the algorithms and I found three part of it: first time

// Read the definitions of the components
  MaxNumberOfCoulombicSites=0;
  LargestNumberOfCoulombicSites=0;
  MaxNumberOfBondDipoleSites=0;
  LargestNumberOfBondDipoleSites=0;
then
// components have been read and the maximum amount of molecules has been determined for NVT
  if(!Swapable)
  {
    // the +1 molecule for the Widom particle insertion particle
    MaxNumberOfCoulombicSites=LargestNumberOfCoulombicSites+2*MaxNumberOfBeads;
    MaxNumberOfBondDipoleSites=LargestNumberOfBondDipoleSites+2*MaxNumberOfBeads;

    Adsorbates=(ADSORBATE_MOLECULE**)calloc(NumberOfSystems,sizeof(ADSORBATE_MOLECULE*));

and then

// default: start with 512 atoms in addition to a possible framework
    MaxNumberOfCoulombicSites=LargestNumberOfCoulombicSites+MAX2(MaxNumberOfBeads,512);
    MaxNumberOfBondDipoleSites=LargestNumberOfBondDipoleSites+MAX2(MaxNumberOfBeads,512);
// default: start with 256 adsorbates
    Adsorbates=(ADSORBATE_MOLECULE**)calloc(NumberOfSystems,sizeof(ADSORBATE_MOLECULE*));
    for(i=0;i<NumberOfSystems;i++)
    {
      MaxNumberOfAdsorbateMolecules=256;
      Adsorbates=(ADSORBATE_MOLECULE*)calloc(MaxNumberOfAdsorbateMolecules,sizeof(ADSORBATE_MOLECULE));
    }

Does the message means that the number of adsorbates exceeds a specific number? does the system stuck in a loop or some thing like that?
#2
Output files / Histograms produced by raspa
August 18, 2019, 09:05:28 AM
Dear Raspa users
I am wondering what are the numbers in produced histograms by RASPA. Just PSD has a definition in the out put file which is:

# column 1: dameter d [A]
# column 2: Connoly distribution
# column 3: PSD
# value at d=0 is void-fraction

while other histograms such as energy histograms and number of adsorbed molecules don't demonstrate any definition nor unit for the numbers in columns. So I don't know if it should be graphs as an simple data group or I manually should make a histogram in excel or libreoffice calc. would you please some one told me what are below numbers for example?
0           0.000715
0.945455   0.007865
1.96364   0.0401225
2.98182   0.125647
4           0.312758
4.94545   0.617705
5.96364   1.01362
6.98182   1.39516
8           1.67574
8.94545   1.81924
9.96364   1.76875
10.9818   1.52925
12           1.23338
12.9455   0.889927
13.9636   0.575767
14.9818   0.346307
16           0.196103
16.9455   0.105903
17.9636   0.05324
18.9818   0.0246125
20           0.0120725
20.9455   0.0036025
21.9636   0.001595
22.9818   0.000715
24           0.0001375
24.9455   0.000055
25.9636   0.0000275
or for example in the next I guess the first column may be the energy interval (bin) but what is the data column actually?
-92000 9.54298e-09
-89300 9.54298e-09
-89075 9.54298e-09
-87950 9.54298e-09
-87725 9.54298e-09
-86825 2.8629e-08
-86375 9.54298e-09
-86150 1.9086e-08
-85700 2.8629e-08
-85475 1.9086e-08
-85250 2.8629e-08
-85025 1.9086e-08
-84800 1.9086e-08
-84575 1.9086e-08
-84350 2.8629e-08
-84125 2.8629e-08
-83900 2.8629e-08
-83675 4.77149e-08
-83450 3.81719e-08
-83225 2.8629e-08
-83000 3.81719e-08
-82775 3.81719e-08
-82550 5.72579e-08
-82325 7.63439e-08
-82100 1.04973e-07
-81875 1.9086e-08
-81650 1.9086e-08
-81425 3.81719e-08
-81200 9.54298e-09
-80975 8.58869e-08
-80750 6.68009e-08
-80525 4.77149e-08
-80300 5.72579e-08
-80075 8.58869e-08
-79850 6.68009e-08
-79625 1.24059e-07
-79400 5.72579e-08
-79175 8.58869e-08
-78950 1.24059e-07
-78725 1.43145e-07
-78500 8.58869e-08
-78275 1.9086e-07
-78050 1.62231e-07
-77825 1.43145e-07
-77600 2.29032e-07
-77375 1.9086e-07
-77150 1.24059e-07
-76925 2.29032e-07
-76700 1.24059e-07
-76475 1.43145e-07
-76250 2.00403e-07
-76025 1.24059e-07
-75800 1.9086e-07
-75575 2.29032e-07
-75350 1.81317e-07
-75125 3.62633e-07
-74900 4.86692e-07
-74675 3.24461e-07
-74450 3.14918e-07
-74225 2.76747e-07
-74000 2.95833e-07
-73775 4.67606e-07
-73550 4.4852e-07
-73325 4.86692e-07
-73100 5.53493e-07
-72875 4.67606e-07
-72650 6.20294e-07
-72425 5.4395e-07
-72200 6.29837e-07
-71975 7.72982e-07
-71750 6.87095e-07
-71525 8.49326e-07
-71300 7.3481e-07
-71075 7.53896e-07
-70850 1.04019e-06
-70625 1.0211e-06
-70400 9.25669e-07
-70175 1.01156e-06
-69950 1.23104e-06
-69725 1.07836e-06
-69500 1.2883e-06
-69275 1.14516e-06
-69050 1.26922e-06
-68825 1.2883e-06
-68600 1.3551e-06
-68375 1.30739e-06
-68150 1.50779e-06
-67925 1.60322e-06
-67700 1.25967e-06
-67475 1.61276e-06
-67250 1.44099e-06
-67025 1.75591e-06
-66800 1.89905e-06
-66575 1.8418e-06
-66350 1.66048e-06
-66125 1.87042e-06
-65900 1.79408e-06
-65675 2.00403e-06
-65450 2.109e-06
-65225 2.15671e-06
-65000 2.56706e-06
-64775 2.18534e-06
-64550 2.29986e-06
-64325 2.72929e-06
-64100 2.9297e-06
-63875 2.60523e-06
-63650 3.07284e-06
-63425 3.29233e-06
-63200 2.9297e-06
-62975 3.1301e-06
-62750 3.27324e-06
-62525 3.25416e-06
-62300 3.48319e-06
-62075 3.54045e-06
-61850 3.78856e-06
-61625 4.17028e-06
-61400 4.17028e-06
-61175 3.98897e-06
-60950 4.30389e-06
-60725 4.63789e-06
-60500 4.80966e-06
-60275 4.65698e-06
-60050 5.21047e-06
-59825 5.3727e-06
-59600 5.62082e-06
-59375 5.5731e-06
-59150 5.65899e-06
-58925 6.16477e-06
-58700 5.89756e-06
-58475 6.29837e-06
-58250 6.77552e-06
-58025 6.82323e-06
-57800 7.22404e-06
-57575 7.4149e-06
-57350 7.29084e-06
-57125 7.93976e-06
-56900 8.10199e-06
-56675 8.57914e-06
-56450 8.38828e-06
-56225 8.44554e-06
-56000 9.54298e-06
-55775 9.09446e-06
-55550 9.25669e-06
-55325 9.81019e-06
-55100 9.71476e-06
-54875 1.0545e-05
-54650 1.07931e-05
-54425 1.13562e-05
-54200 1.21482e-05
-53975 1.15756e-05
-53750 1.2759e-05
-53525 1.25395e-05
-53300 1.17951e-05
-53075 1.25395e-05
-52850 1.28735e-05
-52625 1.34938e-05
-52400 1.3885e-05
-52175 1.38469e-05
-51950 1.44576e-05
-51725 1.52974e-05
-51500 1.55932e-05
-51275 1.50875e-05
-51050 1.57555e-05
-50825 1.60799e-05
-50600 1.66907e-05
-50375 1.75018e-05
-50150 1.74923e-05
-49925 1.77404e-05
-49700 1.88951e-05
-49475 1.91051e-05
-49250 1.8981e-05
-49025 1.98303e-05
-48800 2.01452e-05
-48575 2.01548e-05
-48350 2.08514e-05
-48125 2.17103e-05
-47900 2.13763e-05
-47675 2.20634e-05
-47450 2.20157e-05
-47225 2.23878e-05
-47000 2.31131e-05
-46775 2.41056e-05
-46550 2.41342e-05
-46325 2.47545e-05
-46100 2.48118e-05
-45875 2.58329e-05
-45650 2.56993e-05
-45425 2.57279e-05
-45200 2.63005e-05
-44975 2.72166e-05
-44750 2.61669e-05
-44525 2.71498e-05
-44300 2.80564e-05
-44075 2.80755e-05
-43850 2.819e-05
-43625 2.88484e-05
-43400 2.87626e-05
-43175 3.07093e-05
-42950 3.06139e-05
-42725 3.08906e-05
-42500 3.13964e-05
-42275 3.12342e-05
-42050 3.11769e-05
-41825 3.16064e-05
-41600 3.37154e-05
-41375 3.31905e-05
-41150 3.16541e-05
-40925 3.30378e-05
-40700 3.37822e-05
-40475 3.32668e-05
-40250 3.29519e-05
-40025 3.45933e-05
-39800 3.36867e-05
-39575 3.39539e-05
-39350 3.57957e-05
-39125 3.4641e-05
-38900 3.53568e-05
-38675 3.52613e-05
-38450 3.59198e-05
-38225 3.53758e-05
-38000 3.65401e-05
-37775 3.71127e-05
-37550 3.71031e-05
-37325 3.5748e-05
-37100 3.63301e-05
-36875 3.62443e-05
-36650 3.71127e-05
-36425 3.65305e-05
-36200 3.65878e-05
-35975 3.5643e-05
-35750 3.79143e-05
-35525 3.78284e-05
-35300 3.69123e-05
-35075 3.67882e-05
-34850 3.79238e-05
-34625 3.60343e-05
-34400 3.62061e-05
-34175 3.55476e-05
-33950 3.62633e-05
-33725 3.67214e-05
-33500 3.75898e-05
-33275 3.80574e-05
-33050 3.6521e-05
-32825 3.58148e-05
-32600 3.62633e-05
-32375 3.64447e-05
-32150 3.49846e-05
-31925 3.55572e-05
-31700 3.42689e-05
-31475 3.33718e-05
-31250 3.31142e-05
-31025 3.44215e-05
-30800 3.36867e-05
-30575 3.24652e-05
-30350 3.29519e-05
-30125 3.38394e-05
-29900 3.24366e-05
-29675 3.33527e-05
-29450 3.23316e-05
-29225 3.31142e-05
-29000 3.17495e-05
-28775 3.09956e-05
-28550 3.14155e-05
-28325 2.97073e-05
-28100 3.02608e-05
-27875 3.01463e-05
-27650 2.9526e-05
-27425 2.87626e-05
-27200 2.8085e-05
-26975 2.83045e-05
-26750 2.71498e-05
-26525 2.60619e-05
-26300 2.66631e-05
-26075 2.69971e-05
-25850 2.5976e-05
-25625 2.48213e-05
-25400 2.56325e-05
-25175 2.46782e-05
-24950 2.48022e-05
-24725 2.50217e-05
-24500 2.42106e-05
-24275 2.44491e-05
-24050 2.34089e-05
-23825 2.26169e-05
-23600 2.2636e-05
-23375 2.20252e-05
-23150 2.03266e-05
-22925 1.95059e-05
-22700 1.87329e-05
-22475 1.81317e-05
-22250 1.79694e-05
-22025 1.79885e-05
-21800 1.79122e-05
-21575 1.65952e-05
-21350 1.68625e-05
-21125 1.67002e-05
-20900 1.6977e-05
-20675 1.67479e-05
-20450 1.61276e-05
-20225 1.50588e-05
#3
Dear all
I did some MC simulation to reproduce water adsorption isotherms on MOF-801 but results are not consistent at all. in the literature, water uptake at p/p0=0.2 is about 200 cm3/gr while mine is 0.5 cm3/gr. Molecule and force field definition is the same as literature. Partial charges were found beforehand using Qeq module and finalP1.cif file were used as the input cif. I also changed void fraction up to 0.9 but the impact is not so much! what did I miss? I appreciate any comment.
Regards

P. S. simulation file is as below:

SimulationType                MonteCarlo
NumberOfCycles                50000
NumberOfInitializationCycles  10000
PrintEvery                    10000
RestartFile                   no

chargemethod            Ewald
Forcefield                    GenericMOFs
UseChargesFromCIFFile         yes
cutoffvdw                     12.0
SymmetrizeFrameworkCharges    yes

Framework 0
FrameworkName mof-801-p1
UnitCells 2 2 2
HeliumVoidFraction 0.49
ExternalTemperature 298
ExternalPressure 3456

Component 0 MoleculeName             water
            MoleculeDefinition       TraPPE
            randomTranslationProbability   0.5
            RotationProbability      0.5
            ReinsertionProbability   0.5
            SwapProbability          1.0
            CreateNumberOfMolecules  0