Inconsistency Between Results in Restart and Output Files

[Lingxiao Qin]

Dear Prof. Dubbeldam and RASPA community,

The "Restart and Crash-Recovery" section of the RASPA manual mentions that "The restart file is written at 'PrintEvery' intervals.". According to this statement, I expect that the positions, velocities and forces of the adsorbate atoms recorded in the restart file to match the results printed at the last "PrintEvery" interval in the output file. However, a test simulation shows that the number of adsorbates in the restart file (seven, see the snippet attached below) differs from that reported at the last "PrintEvery" interval in the output file (nine, see the snippet attached below), which makes me confused. Could you please clarify what is the relationship between the configuration recorded by the restart file and the results documented in the output file?

Here are my simulation.input and snippets of restart and output files.

simulation.input

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SimulationType                MonteCarlo
NumberOfCycles                1000
NumberOfInitializationCycles  1000
PrintEvery                    200

ContinueAfterCrash no

ChargeMethod                  Ewald
Forcefield                    ExampleMOFsForceField
UseChargesFromCIFFile yes
CutOffVDW                     10
CutOffChargeCharge            10
RemoveAtomNumberCodeFromLabel yes

Framework             0
FrameworkName         Cu-BTC
UnitCells             1 1 1
HeliumVoidFraction    0.745895
ExternalTemperature   273
ExternalPressure    2500000.0


Component 0 MoleculeName              N2
            MoleculeDefinition        ExampleDefinitions
            TranslationProbability    1.0
            RotationProbability       1.0
            ReinsertionProbability    1.0
            SwapProbability           1.0
            CreateNumberOfMolecules   0
restart_Cu-BTC_1.1.1_273.000000_2.5e+06

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Components: 1 (Adsorbates 7, Cations 0)
========================================================================
Component 0 (N2)
Fractional-molecule-id component 0: -1
Lambda-factors component 0:  0.000000 0.000000 0.000000
Number-of-biasing-factors component 0: 21
Biasing-factors component 0:  0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
Maximum-CF-Lambda-change component 0: 0.500000
Maximum-CBCF-Lambda-change component 0: 0.500000

Maximum-translation-change component 0: 1.000000,0.487500,1.000000
Maximum-translation-in-plane-change component 0: 0.000000,0.000000,0.000000
Maximum-rotation-change component 0: 0.490874 1.472622 0.490874

Reactions: 0

Component: 0     Adsorbate    7 molecules of N2
------------------------------------------------------------------------
output_Cu-BTC_1.1.1_273.000000_2.5e+06.data

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Current cycle: 800 out of 1000
========================================================================================================

Net charge: 1.0103e-13 (F: 1.0103e-13, A: 0, C: 0)
Current Box:  26.34300   0.00000   0.00000 [A]   Average Box:  26.34300   0.00000   0.00000 [A]
               0.00000  26.34300   0.00000 [A]                  0.00000  26.34300   0.00000 [A]
               0.00000   0.00000  26.34300 [A]                  0.00000   0.00000  26.34300 [A]
Box-lengths:   26.34300  26.34300  26.34300 [A] Average:  26.34300  26.34300  26.34300 [A]
Box-angles:   90.00000  90.00000  90.00000 [degrees] Average:  90.00000  90.00000  90.00000 [degrees]
Volume: 18280.82098 [A^3] Average Volume: 18280.82098 [A^3]

Loadings per component:
----------------------------------------------------------------------------------------------------------------------------------------------------
Component 0 (N2), current number of integer/fractional/reaction molecules: 9/0/0 (avg.   9.08489), density:  22.90147 (avg.  23.11749) [kg/m^3]
absolute adsorption:   9.00000 (avg.   9.08489) [mol/uc],   0.9302462147 (avg.   0.9390209050) [mol/kg],  26.0594337300 (avg.  26.3052433421) [mg/g]
                      20.8505160951 (avg.  21.0471917914) [cm^3 STP/g],   18.3237652830 (avg.  18.4966070141) [cm^3 STP/cm^3]
excess adsorption:    -0.1951236435 (avg.  -0.1102297608) [mol/uc],  -0.0201681145 (avg.  -0.0113934242) [mol/kg],  -0.5649790729 (avg.  -0.3191694608) [mg/g]
                      -0.4520476299 (avg.  -0.2553719336) [cm^3 STP/g],   -0.3972666493 (avg.  -0.2244249183) [cm^3 STP/cm^3]
----------------------------------------------------------------------------------------------------------------------------------------------------
Degrees of freedom: 45 0 45 0
Number of Framework-atoms:    624
Number of Adsorbates:           9 (9 integer, 0 fractional, 0 reaction)
Number of Cations:              0 (0 integer, 0 fractional, 0 reaction)

Current total potential energy:             -3908.4716378953 [K]  (avg.       -3915.5804048016)
Current Host-Host energy:                     0.0000000000 [K]  (avg.           0.0000000000)
Current Host-Adsorbate energy:            -3762.2229554409 [K]  (avg.       -3738.1974921185)
Current Host-Cation energy:                   0.0000000000 [K]  (avg.           0.0000000000)
Current Adsorbate-Adsorbate energy:        -146.2486824543 [K]  (avg.        -177.3829126831)
Current Cation-Cation energy:                 0.0000000000 [K]  (avg.           0.0000000000)
Current Adsorbate-Cation energy:              0.0000000000 [K]  (avg.           0.0000000000)



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Finishing simulation
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