Author Topic: Error in connectivity  (Read 417 times)

Monica_Gao

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Error in connectivity
« on: December 02, 2020, 09:21:04 AM »
Dear Professor David,
    When I calculate the Rosenbluth Weight of water in a box with a size of 30 * 30 * 30, it fails and shows "No atoms can be grown, check the connectivity of your molecule", Could you tell me how to sovle this problem? It happends in both the water defination files defined by me and the original file in RASPA.

The file defined by me:

# critical constants: Temperature [T], Pressure [Pa], and Acentric factor [-]
647.14
22064000.0
-0.217000
# Number Of Atoms
4
# Number Of Groups
1
# H2O-group
rigid
# number of atoms
4
0 Ow      -3.0782    0.8693    0.7624
1 Hw      -3.3972    1.5074    1.4005
2 Hw     -2.1210    0.8693    0.7624
3 Lw      -3.0064    0.9436    0.8327
# Chiral centers Bond  BondDipoles Bend  UrayBradley InvBend  Torsion Imp. Torsion Bond/Bond Stretch/Bend Bend/Bend Stretch/Torsion Bend/Torsion IntraVDW IntraCoulomb
               0    2            0    0            0       0        0            0         0            0         0               0            0        0            0
# Bond stretch: atom n1-n2, type, parameters
0 1 RIGID_BOND
0 2 RIGID_BOND
# Number of config moves
0


The original file in RASPA

# critical constants: Temperature [T], Pressure [Pa], and Acentric factor [-]
647.14
22064000.0
-0.217000
# Number Of Atoms
3
# Number Of Groups
1
# H2O-group
rigid
# number of atoms
3
0 Ow  0.8660  -0.5000   0.0000
1 Hw  1.7321  -0.0000   0.0000
2 Hw   0.0000   0.0000   0.0000       
# Chiral centers Bond  BondDipoles Bend  UrayBradley InvBend  Torsion Imp. Torsion Bond/Bond Stretch/Bend Bend/Bend Stretch/Torsion Bend/Torsion IntraVDW IntraCoulomb
               0    2            0    0            0       0        0            0         0            0         0               0            0        0            0
# Bond stretch: atom n1-n2, type, parameters
0 1 RIGID_BOND
0 2 RIGID_BOND
# Number of config moves
0

Another thing it that, some articles published in journals involves multi-component adsorption, but I tried yestaday, but it failed with an error, so could you please tell me how to work it out?

I will be very grateful if you give me some instructions and advices, thank you very much.
Best Regard,
Monica Gao.

Monica_Gao

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Re: Error in connectivity
« Reply #1 on: December 02, 2020, 09:30:55 AM »
Dear professor David,
  I have found the mistakes in both water definition files, so if you read this problem please ignore the first question and to the second question.
  Could you please give me some advices to calculate multi-component adsorption with at least three components?
  I am very grateful and look forward to your answer.

Best regard.
Monica, Gao

David Dubbeldam

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Re: Error in connectivity
« Reply #2 on: December 23, 2020, 09:23:51 PM »
Check the manual and examples. There are explicit examples for mixtures and adsorption mixtures,
for example:
examples/Basic/MC_BinaryMixture_in_Box
examples/Non-Basic/Adsorption_of_Binary_mixture_CO2_CH4_in_IRMOF-1

Monica_Gao

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Re: Error in connectivity
« Reply #3 on: December 27, 2020, 08:46:41 AM »
Dear professor David,
Thank you very much. And Merry Chrisma  ;D