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1
Output files / Histograms produced by raspa
« Last post by Mozhdeh on August 18, 2019, 08:05:28 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
2
Input files and parameters / Partial atomic charges in molecule.def file?
« Last post by small_pawn on August 13, 2019, 02:29:58 PM »
Hi there,

I would like to ask whether it is possible to define atomic charges in a molecule.def file so that they will overwrite those in the FF file pseudo_atoms.def? I need something similar to that in a cif file that can for instance overwrite charges from pseudo_atoms.def if stated in the input.

Something like (in the coordinate section of a molecule.def):
# atomic positions
0   ff_type     atom_x      atom_y    atom_z      atom_q
...

Best,
Rada
3
General / Thank you so much for helping
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4
General / Status of iRASPA-QT
« Last post by petersbk on August 02, 2019, 02:25:56 PM »
The iRASPA-QT project is visible on github. What is the status? Is it usable on linux at this time?
Thanks.
5
Thanks for your response.
So it is correct that I randomly translate the cation Na in FAU if my model can reproduce the certain "occupancy"
To reliably model adsorption/diffusion, the mobility of the cations needs to be taken into account. For example, in FAU there are many different cation-sites with certain "occupancy" ratios. Your cation model needs to be able to reproduce that.
That is why it is hard to reach an equilibrated system and it is a good idea to, when you have generated that, to store these positions in a restart-file.
Since cations are charged, the usual CBMC biasing can lead to numerical issues, but for single-atom cations you can achieve the same with a random-translation that tries to place the cation randomly in the box.
Look in the literature for papers on modeling of zeolites with cations for more pointers.
6
To reliably model adsorption/diffusion, the mobility of the cations needs to be taken into account. For example, in FAU there are many different cation-sites with certain "occupancy" ratios. Your cation model needs to be able to reproduce that.
That is why it is hard to reach an equilibrated system and it is a good idea to, when you have generated that, to store these positions in a restart-file.
Since cations are charged, the usual CBMC biasing can lead to numerical issues, but for single-atom cations you can achieve the same with a random-translation that tries to place the cation randomly in the box.
Look in the literature for papers on modeling of zeolites with cations for more pointers.
7
Hi, I was read the RASPA doc and have some confuse in “Example 4: Adsorption of CO2 in Na-LTA” in Page 98 :

    1.the guide says "it is important to start from crystallographic position ", but the example use "RestartFile no". So I am confuse how to define position with my cif while keep it's "Cation attribute" in Raspa. Should I run a simulation to generate random cation position in a restart file, and then substitute the cations position from cif?
    2.the guide also says "use only translation for the ions" and "Reinsertion moves may transport the ions to positions in the windows and this is especially important for diffusion".  Does the "reinsertion" is one kind of "translation"(equal to randomtranslation here,right?)?  Since we already take a cation position from cif,why should we randomly change them positon to make the cif position meaningness?
    3.the Example 5 also says "the ions are read from the restart file" but the "RestartFile no" still exists below. Is that some mistake?

thanks for your time and I will appreciate it if someone response my question
8
Output files / Re: different adsorption isotherms compare to literature
« Last post by David Dubbeldam on July 24, 2019, 01:14:18 PM »
What do you mean with "there were no more than 2 number of adsorbent in each cycle", do you have multiple frameworks? do you mean "adsorbent" which is the framework, or "adsorbate" which means the molecules inside the framework.
"So I think something wrong about the water, maybe the increased charge of it in the MC simulation.", have you tried making it charge-neutral?
9
Output files / Re: different adsorption isotherms compare to literature
« Last post by Mozhdeh on July 21, 2019, 06:04:36 AM »
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
10
Output files / Re: different adsorption isotherms compare to literature
« Last post by Mozhdeh on July 20, 2019, 12:55:19 PM »
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


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