Messages

Thanks for the fast respond.
For me, It seems that the run stuck in the initialization part. It takes two days for a structure with more than 2600 atoms and nothing happens after appearance of this message. And actually I found out that running simultaneous jobs of 1 structure with different conditions, for example different pressures, gives wrong results. So the jobs should be run individually. Since I am using a 6-core system (each with 2 thread)  with 16 GB of memory I wonder, Is there a way to manage memory allocation to use the total power of a given PC?
Regards

[Dear Pro. DubbledamI have encounter a message from program as:]

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?

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

Dear all
I test the same MOF adsorption isotherm of N2 at 77 K which behaved normal


Current cycle: 40000 out of 50000
========================================================================================================

Net charge: 0.000176 (F: 0.000176, A: 0, C: 0)
Current Box:  35.66960   0.00000   0.00000 [A]   Average Box:  35.66960   0.00000   0.00000 [A]
               0.00000  35.66960   0.00000 [A]                  0.00000  35.66960   0.00000 [A]
               0.00000   0.00000  35.66960 [A]                  0.00000   0.00000  35.66960 [A]
Box-lengths:   35.66960  35.66960  35.66960 [A] Average:  35.66960  35.66960  35.66960 [A]
Box-angles:   90.00000  90.00000  90.00000 [degrees] Average:  90.00000  90.00000  90.00000 [degrees]
Volume: 45383.15846 [A^3] Average Volume: 45383.15846 [A^3]

Loadings per component:
----------------------------------------------------------------------------------------------------------------------------------------------------
Component 0 (N2), current number of integer/fractional/reaction molecules: 302/0/0 (avg. 298.25187), density: 309.54848 (avg. 305.70667) [kg/m^3]
   absolute adsorption:  37.75000 (avg.  37.28148) [mol/uc],   6.3438084017 (avg.   6.2650752004) [mol/kg], 177.7121497852 (avg. 175.5065588236) [mg/g]
                        142.1899676634 (avg. 140.4252435976) [cm^3 STP/g],  247.6738366201 (avg. 244.5999490094) [cm^3 STP/cm^3]
   excess adsorption:    37.7474627383 (avg.  37.1564835879) [mol/uc],   6.3433820202 (avg.   6.2440692123) [mol/kg], 177.7002053553 (avg. 174.9181079965) [mg/g]
                        142.1804107585 (avg. 139.9544158901) [cm^3 STP/g],  247.6571899091 (avg. 243.7798369677) [cm^3 STP/cm^3]
----------------------------------------------------------------------------------------------------------------------------------------------------
Degrees of freedom: 1510 0 1510 0
Number of Framework-atoms:   2624
Number of Adsorbates:         302  (302 integer, 0 fractional, 0 reaction)
Number of Cations:              0 (0 integer, 0 fractional, 0 reaction)

Current total potential energy:           -541892.7820463965 [K]  (avg.     -530686.6081954332)
   Current Host-Host energy:                     0.0000000000 [K]  (avg.           0.0000000000)
   Current Host-Adsorbate energy:          -484779.4158412396 [K]  (avg.     -476688.6897432785)
   Current Host-Cation energy:                   0.0000000000 [K]  (avg.           0.0000000000)
   Current Adsorbate-Adsorbate energy:      -57113.3662051579 [K]  (avg.      -53997.9184521721)
   Current Cation-Cation energy:                 0.0000000000 [K]  (avg.           0.0000000000)
   Current Adsorbate-Cation energy:              0.0000000000 [K]  (avg.           0.0000000000)

WARNING: THE SYSTEM HAS A NET CHARGE


So I think something wrong about the water, maybe the increased charge of it in the MC simulation. Any comment?
Best regards

Dear Dr. Dubbeldam
Thanks for the kind response. Actually I compare it with both simulated and experimental results which are consistent in previous literature. I compare my output with the examples of RASPA2 and I noticed that there were no more than 2 number of adsorbent in each cycle, while for example in the Adsorption_of_CO2_in_Flexible_IRMOF-1_Fixed_Volume, number of adsorbents in the last cycle is 39 and the excess loading is 140.3574056061 (avg. 158.7275906778) [cm^3 STP/g]. So I think there is something inhibiting a proper MC simulation. Moreover, I used psuedo_atom.def file to neutralized the charge of water molecules, however the MOF itself has a net charge. So I used randomTranslationProbability   0.5 and ReinsertionProbability   0.0 , but in the MC moves, charges were created on the water molecules (Net charge: 0.964176 (F: 0.000176, A: 0.964, C: 0)).

Here is the properties calculated at the last cycle of my simulation:

[Init] Current cycle: 900000 out of 1000000
========================================================================================================

Net charge: 0.964176 (F: 0.000176, A: 0.964, C: 0)
Current Box:  35.66960   0.00000   0.00000 [A]
               0.00000  35.66960   0.00000 [A]
               0.00000   0.00000  35.66960 [A]
Box-lengths:  35.66960  35.66960  35.66960 Box-angles:   90.00000  90.00000  90.00000 [degrees]
Volume: 45383.15846 [A^3]

Loadings per component:
----------------------------------------------------------------------------------------------------------------------------------------------------
Component 0 (water), current number of integer/fractional/reaction molecules: 2/0/0, density:   1.31729 [kg/m^3]
   absolute adsorption:   0.25000 [mol/uc],         0.0420 [mol/kg],              0.7563 [mg/g]
                                                    0.9417 [cm^3 STP/g],          1.6402 [cm^3 STP/cm^3]
   excess adsorption:     0.25000 [mol/uc],         0.0420 [mol/kg],              0.7563 [mg/g]
                                                    0.9417 [cm^3 STP/g],          1.6402 [cm^3 STP/cm^3]
----------------------------------------------------------------------------------------------------------------------------------------------------
Degrees of freedom: 12 0 12 0
Number of Framework-atoms:   2624
Number of Adsorbates:           2 (2 integer, 0 fractional, 0 reaction)
Number of Cations:              0 (0 integer, 0 fractional, 0 reaction

Current total potential energy:            -12224.3694682955 [K]
   Current Host-Host energy:                     0.0000000000 [K]
   Current Host-Adsorbate energy:           -14790.5805795910 [K]
   Current Host-Cation energy:                   0.0000000000 [K]
   Current Adsorbate-Adsorbate energy:        2566.2111112939 [K]
   Current Cation-Cation energy:                 0.0000000000 [K]
   Current Adsorbate-Cation energy:              0.0000000000 [K]

WARNING: THE SYSTEM HAS A NET CHARGE

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