iraspa / raspa2

Classical molecular simulation code

RASPA2

This software is a general purpose classical simulation package. It has been developed at Northwestern University (Evanston, USA) during 2006-2011 in active collaboration with University Pablo de Olavide (Seville, Spain), and the Technical University of Delft.

It can be used for the simulation of molecules in gases, fluids, zeolites, aluminosilicates, metal-organic frameworks, carbon nanotubes and external fields.

Documentation: https://iraspa.org/raspa/

References

• D. Dubbeldam, S. Calero, D.E. Ellis, and R.Q. Snurr, "RASPA: Molecular Simulation Software for Adsorption and Diffusion in Flexible Nanoporous Materials", Mol. Sim., 42 (2), 81-101, 2016. link to article
• D. Dubbeldam, A. Torres-Knoop, and K.S. Walton, "On the Inner Workings of Monte Carlo Codes", Mol. Sim. (special issue on Monte Carlo) 39(14-15), 1253-1292, 2013. link to article
• D. Dubbeldam and R.Q. Snurr, "Recent developments in the molecular modeling of diffusion in nanoporous materials", Mol. Sim., 33 (4-5), 305-325, 2007. link to article
• D. Dubbeldam, K.S. Walton, T.J.H. Vlugt, and S. Calero, "Design, Parameterization, and Implementation of Atomic Force Fields for Adsorption in Nanoporous Materials", Adv. Theory Simulat., 2(11), 1900135, 2019. link to article

Force fields used as examples in RASPA

Note: all force field-, structure-, and molecule-files are meant as examples to illustrate the input and workings of the code. For simulations on your own systems, you will have to construct your own classical force field and validate it. The force fields used in the examples are based on the following force fields taken from literature:

small adsorbates

• CO2 using a shifted LJ potential (can be used both in Monte Carlo and in Molecular Dynamics).
  "Transferable Force Field for Carbon Dioxide Adsorption in Zeolites", A. Garcia-Sanchez, C. O. Ania, J. B. Parra, D. Dubbeldam, T. J. H. Vlugt, R. Krishna, S. Calero, J. Phys. Chem. C 2009, 113, 8814-8820. link to article
• N2, O2, and Ar using shifted LJ potentials (can be used both in Monte Carlo and in Molecular Dynamics).
  "Effect of air humidity on the removal of carbon tetrachloride from air using Cu–BTC metal–organic framework", A. Martin-Calvo, E. Garcia-Perez, A. Garcia-Sanchez, R. Bueno- Perez, S. Hamad, S. Calero, Phys. Chem. Chem. Phys. 2011, 13, 11165-11174. link to article
• CH4 using shifted LJ potentials (can be used both in Monte Carlo and in Molecular Dynamics).
  "Effect of pressure, membrane thickness, and placement of control volumes on the flux of methane through thin silicalite membranes: A dual control volume grand canonical molecular dynamics study", M. G. Martin, A. P. Thompson, T. M. Nenoff, J. Chem. Phys. 2001, 114, 7174-7181. link to article
• Helium potential for computing void-fractions.
  J.O. Hirschfelder, C.F. Curtiss, R.B. Bird, Molecular Theory of Gases and Liquids, Wiley, New York, 1954, p. 1114. reference in article
• Linear/Branched alkane model.
  "United atom force field for alkanes in nanoporous materials", D. Dubbeldam, S. Calero, T.J.H. Vlugt, R. Krishna, T.L.M. Maesen, B. Smit, J. Phys. Chem. B 2004, 108(33), 12301-12313 link to article

rigid MOFs

• "DREIDING: a generic force field for molecular simulations", S.L. Mayo, B.D. Olafson, W.A. Goddard, J. Phys. Chem. 1990, 94, 8897-8909 link to article
• "UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations", A.K. Rappé, C.J. Casewit, K.S. Colwell, W.A. Goddard, W.M. Skiff, J. Am. Chem. Soc. 1992, 114, 10024-10035. link to article

rigid zeolites

• "TraPPE-zeo: Transferable Potentials for Phase Equilibria Force Field for All-Silica Zeolites", P. Bai, M. Tsapatsis, J. I. Siepmann, J. Phys. Chem. C 2013, 117, 24375-24387. link to article

flexible MOFs

• Flexible force fields for IRMOF-1, IRMOF-10, and IRMOF-16. "Exceptional Negative Thermal Expansion in Isoreticular Metal–Organic Frameworks", D. Dubbeldam, K.S. Walton, D.E. Ellis, R.Q. Snurr, Angew. Chem. Int. Ed. 2007, 46, 4496-4499. link to article

flexible zeolites

• "Molecular dynamics studies on zeolites. 3. Dehydrated zeolite A", P. Demontis, G. B. Suffritti, S. Quartieri, E. S. Fois, A. Gamba, J. Phys. Chem. 1988, 92, 867-871. link to article
• "Molecular modeling of zeolite structure. 2. Structure and dynamics of silica sodalite and silicate force field", J. B. Nicholas, A. J. Hopfinger, F. R. Trouw, L. E. Iton, J. Am. Chem. Soc. 1991, 113, 4792-4800. link to article
• "Potential Functions for Silica and Zeolite Catalysts Based on ab Initio Calculations. 3. A Shell Model Ion Pair Potential for Silica and Aluminosilicates", K.-P. Schröder, J. Sauer, J. Phys. Chem. 1996, 110, 11043-11049. link to article

Acknowledgements

Development of this work is partially supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences through the Nanoporous Materials Genome Center under award DE-FG02-17ER16362.

Installation

rm -rf autom4te.cache  
mkdir m4  
aclocal  
autoreconf -i  
automake --add-missing  
autoconf  

./configure --prefix=${RASPA_DIR}  
# or ./scripts/CompileScript/make-gcc-local  

make  
make install  

Conda-forge

raspa2 can be installed through the conda package manager on Linux and MacOS (done by Leopold Talirz):

conda install -c conda-forge raspa2
export RASPA_DIR=/path/to/environment/root
# e.g. export RASPA_DIR=/Users/leopold/Applications/miniconda3/envs/raspa-env

Documentation

Build the latest RASPA manual using:

cd Docs
pdflatex raspa.tex

raspa2's Issues

Some provided MOFs are not charge-balanced

The MIL-88 series of MOFs are provided with a terminal O ligand on each metal. However, in reality, they should all be OH groups. The protons on some of the Zr-MOFs, such as UiO-66, are also missing.

Installation not working in RASPA2 directory

(1) The PDF installation instructions from https://iraspa.org/raspa/ are no longer accurate since this repo clones into 'RASPA2' directory, and no longer 'RASPA'.

(2) In the run script in examples/Basic/1_.../, RASPA_DIR is incorrectly assigned as the RASPA directory instead of the RASPA2 directory

I am still struggling to get a working installation. Do I need to move ${RASPA_DIR}/src/simulate and src/.libs to ${RASPA_DIR}/simulations/bin/ ?

Cannot run "make install" on Mac OS 10.15.7

When I try to "make install" or "sudo make install" on Mac OSX 10.15.7, it gives the error "gmkdir: cannot create directory ‘/lib’: Read-only file system".

I have already gone into Recovery mode and disabled csrutil with "csrutil disable" but am still running into this error after restarting.

I was wondering if there is something else I might have missed that causes this or if there are additional setup steps I need to take to set up RASPA on Mac OS. Thank you!

Could other potential functions be added into RASPA2? like the ReaxFF potential function.

Sometimes, it is found that chemical asdorption behaviors calculated by the potential functions in the RASPA are not accurate, could other potential functions be added into RASPA2, like the ReaxFF potential function.

Thanks

Density plot generation - one plot per site instead of one plot per guest?

Hi there! We are currently developing some codes that involve the use of the density plots generated by GCMC codes. We would like these tools to be compatible with RASPA. Currently, it seems RASPA outputs two plots per guest in the simulation: a single plot for the entire guest (all guest atoms) and a plot for only the COM. Our code relies on a probability plot for each guest atom. Would it be possible to implement a VTK density plot for each site in each guest atom as ouput? As it stands, I see no way to deconvolute the total plot into a plot for each site, except by subtracting the COM data from the total. But this will only work for guests where there is an atom at the COM and where there are no more than two sites. Thus, it will work for CO2, but not (for example) H2O.

empty changelog?

The changelog file committed to the repository is empty
https://github.com/iRASPA/RASPA2/blob/master/ChangeLog

Has a changelog been kept?
If not, perhaps it would be worth autogenerating one from the git commit messages (& release tags)?

Charge Equilibration leads to Segmentation Fault

Hello everyone!

I have been using RASPA for the past few months, and recently I started incorporating the charge equilibration feature in my simulation pipeline. Initially, everything went fine, but then I started having problems.

When the ChargeFromChargeEquilibration option is set to yes, the simulation crashes with a Segmentation Fault for some (but not all) CIF files.

One example of a CIF file that leads to a crash is TER.cif from the Database of Zeolite Structures: https://asia.iza-structure.org/IZA-SC/cif/TER.cif.

The simulation.input file is as simple as

SimulationType                  MonteCarlo
NumberOfCycles                  0
Framework                       0
FrameworkName                   TER
UnitCells                       3 2 2

ChargeFromChargeEquilibration   yes
ChargeEquilibrationPeriodic     yes
ChargeEquilibrationEwald        yes
SymmetrizeFrameworkCharges      no

The purpose of this MonteCarlo simulation is simply to create a new CIF file containing a 3x2x2 supercell with P1 symmetry.

To help with debugging, I recompiled RASPA v2.0.39 with CFLAGS="-w -ggdb -O0" and executed

$ gdb ~/RASPA2-2.0.39/bin/simulate

(gdb) run
Starting program: ~/RASPA2-2.0.39/bin/simulate
Program received signal SIGSEGV, Segmentation fault.
0x00007ffff6492e18 in __strcpy_sse2_unaligned () from /lib64/libc.so.6

(gdb) bt
#0  0x00007ffff6492e18 in __strcpy_sse2_unaligned () from /lib64/libc.so.6
#1  0x00007ffff718e543 in WriteFrameworkDefinitionShell (string=0x7ffff7bff6f8 "initial") at framework.c:2103
#2  0x00007ffff793de5e in run (inputData=0x408910 "simulation.input", inputCrystal=0x408930 "", 
    raspaDir=0x7fffffffd8cb "~/RASPA2-2.0.39/", stream=false) at run.c:101
#3  0x00000000004013e1 in main (argc=1, argv=0x7fffffffd398) at main.c:106

(gdb) frame 1
#1  0x00007ffff718e543 in WriteFrameworkDefinitionShell (string=0x7ffff7bff6f8 "initial") at framework.c:2103
2103	        strcpy(symbol,PseudoAtoms[Type].ChemicalElement);

(gdb) p Type
$2 = -415391835

(gdb) p PseudoAtoms[Type].ChemicalElement
Cannot access memory at address 0xffffffce7b817de4

The source of the Segmentation Fault seems to be that we are trying to access the PseudoAtoms array at a negative index (Type = -415391835), which does not exist. This occurs at https://github.com/iRASPA/RASPA2/blob/master/src/framework.c#L2103.

So I investigated further why/where the Type index variable was set to a negative value and found it at https://github.com/iRASPA/RASPA2/blob/master/src/framework.c#L2101.

(gdb) p CurrentSystem
$3 = 0

(gdb) p CurrentFramework
$4 = 0

(gdb) p i
$5 = 0

(gdb) p Framework[CurrentSystem].Atoms[CurrentFramework][i].Type
$6 = -415391835

gdb) p Framework[CurrentSystem].Atoms[CurrentFramework][i]
$14 = {
    "Type": -415391835,
    "Charge": 0.10504292071040217,
    "CFVDWScalingParameter": 0.60642472553108762,
    "CFChargeScalingParameter": -0.79514090088772649,
    "CFStoredScalingParameter": 0.99604382482586074,
    "Modified": 159528,
    "OriginalType": -1078542400,
    "CreationState": -845529396,
    "AssymetricType": 1068764949,
    "temp": 0.99692550651848566,
    "Position": {
        "x": 0.42480330804058136,
        "y": 0.9052856728556895,
        "z": -0.13602553641904541
    },
    "AnisotropicPosition": {
        "x": 0.99070533128772031,
        "y": 0.93363353366682034,
        "z": -0.35822956998662936
    },
    "ReferencePosition": {
        "x": -0.73270495495271304,
        "y": -0.68054643411580806,
        "z": 0.9831752294314593
    },
    "ReferenceAnisotropicPosition": {
        "x": 0.18266490695368287,
        "y": 0.74724584781165182,
        "z": 0.6645476980083872
    },
    "RattleReferencePosition": {
        "x": 0.99913704083225319,
        "y": -0.041535209605439771,
        "z": 0.93363353366682034
    },
    "Velocity": {
        "x": -0.35822956998662936,
        "y": 0.74724584781165182,
        "z": 0.6645476980083872
    },
    "ReferenceVelocity": {
        "x": 0.99913704083225319,
        "y": -0.041535209605439771,
        "z": 0.93363353366682034
    },
    "Force": {
        "x": -0.35822956998662936,
        "y": 0.74724584781165182,
        "z": 0.6645476980083872
    },
    "ReferenceForce": {
        "x": 0.99913704083225319,
        "y": -0.041535209605439771,
        "z": 0.93363353366682034
    },
    "RattleGradient": {
        "x": -0.35822956998662936,
        "y": 0.74724584781165182,
        "z": 0.6645476980083872
    },
    "ElectricField": {
        "x": 0.99913704083225319,
        "y": -0.041535209605439771,
        "z": 0.93363353366682034
    },
    "ReferenceElectricField": {
        "x": -0.35822956998662936,
        "y": 0.75562487546411949,
        "z": 0.65500461645688624
    },
    "InducedElectricField": {
        "x": -0.50000000000000122,
        "y": -0.86602540378443804,
        "z": -0.50000000000000122
    },
    "InducedDipole": {
        "x": -0.86602540378443804,
        "y": -0.50000000000000122,
        "z": -0.86602540378443804
    },
    "HessianIndex": {
        "x": 11,
        "y": -1075838976,
        "z": -396866395
    },
    "HessianAtomIndex": -1075071366,
    "Fixed": {
        "x": -1725695833,
        "y": -1075481023,
        "z": 1040166342
    }
}

I notice that both Type and OriginalType are negative, but AssymetricType is positive.

I have read here several times that is typically something in the CIF files that generates these Segmentation Faults. I also agree that is probably easier to fix the non-standard CIF rather than implementing safeguards in the code to deal with rare situations. I hope that I was able to pinpoint the issue well enough to make it easier for the experts identify its origin. I also posted this in the iRASPA Forum.

Is there anything we can do (preferably) to the CIF file (otherwise, to the code itself) to prevent this Segmentation Fault from happening?

Overestimation of Helium Void Fraction (HVD)

After installation and setup of my venv, when trying to calculate HVD as done in examples/Auxiliary/3_HeliumVoidFraction, the Average Widom Rosenbluth-weight I obtain is around 0.90, which is a 0.09 overestimation to what is usually found experimentally as well as in your outputted files. This result was obtained using the same simulation input and force field files.

This discrepancy goes across different MOF structures as well ( I have not tested this for Zeolites). The output file I obtain from such calculation is attached (here using IRMOF-1 from the CIFs files folder).

output_IRMOF-1_1.1.1_298.000000_0.txt

Problem in declaring RASPA_DIR

RASPA v2.0.37
I recently came up with a weird situation while trying to run calculations in our HPC center. I was declaring the shared directory as:

export RASPA_DIR=path/to/shared/library

Even though the path was exported and available as environmental variable but RASPA could not use it within the calculation. Instead, RASPA was looking for shared files in the directory of:

RASPA_DIR=$HOME/RASPA/simulations

We tried different cases to solve the issue.

1. This solution does not work:

export RASPA_DIR=path/to/shared
unset RASPA2_DIR

2. This solution interestingly works:

export RASPA2_DIR=path/to/shared

Based on the source code:

RASPA2/src/main.c

Lines 57 to 66 in 4467e14

	// set default RASPA_DIR
	raspa_dir = getenv("HOME");
	strcat(raspa_dir,"/RASPA/simulations");
	// get the raspa install directory from environement if defined
	if(getenv("RASPA_DIR")&&(strlen(getenv("RASPA_DIR"))>0))
	raspa_dir=getenv("RASPA_DIR");
	// allow multiple versions of raspa to coexist peacefully by using different dirs
	if(getenv("RASPA2_DIR")&&(strlen(getenv("RASPA2_DIR"))>0))
	raspa_dir=getenv("RASPA2_DIR");

There should not be any issue but I do not know for what is the reason that RASPA is not able to read shared folder if it is declared as RASPA_DIR but it works perfectly when it is declared as RASPA2_DIR.

Unable to run RASPA2 simulation

I have installed RASPA2. However, on trying to run the sample simulation with the run shell script I am having the error

"error while loading shared libraries: libraspa2.so.0: cannot open shared object file: No such file or directory"

RASPA is installed in the the RASPA/simulation directory in home. When I checked the lib directory of the RASPA/simulation it has the following files:
libraspa2.a libraspa2.la libraspa2.so libraspa2.so.0 libraspa2.so.0.0.0

I am new to RASPA2 and I do not have any idea to resolve this issue. I have attached the txt versions of the
run.txt
simulation.input.txt
run.sh and simulation.input file I am using.

Wrong atomtype in TraPPE trans-butene molecule

I found a small mistake

molecules/TraPPE/2-trans-butene.def has a wrong atomtype (3rd atom, index 2). Should be CH_sp2, but it is sp3 instead

LICENSE

It looks like the License here is missing. I'm just seeing "COPYING" in that file

conda package

This is just to let you know that over the coming days I'm going to look into creating a conda package for raspa2.

The goal would be that installing raspa becomes as simple as

conda install -c conda-forge raspa2

on linux and macos.

Python interface `RASPA2.run()` fails for `v2.0.38`

In a Fedora 32 machine, I executed the commands below to install RASPA2 version 2.0.38.

$ dnf install -y automake blas-devel diffutils fftw-devel file gcc-c++ lapack-devel libtool make python3-devel which
$ pip install .

Then I ran

$ python3 -c "import RASPA2; RASPA2.run('Cu-BTC', 'CO2')"

and got

$ ERROR in cif-file: no proper space group definition found

Yet, when I run simulation simulation.input by passing this input file that uses the same Cu-BTC framework CIF file, the simulation works fine.

test suite for continuous integration?

Are there unit / integrations tests that could become the start of a continuous integration test setup?

I'd be happy to set something up on github in case you're interested.

Installation issue

After ./configure when 'make' is given error comes as 'no rule to make target 'all' stop' and further if I use 'make install' then error message comes as 'no rule to make target 'install' stop'. What should I do? I am using windows subsystem for linux to install this.

Ammonia partition function

See attached. We are attempting to reproduce the ammonia reaction equilibrium system with RASPA. We have calculated the partition functions for each element (H2, N2, NH3). However, using the same reference data (McQuarrie), we obtain slightly different results for NH3. Our calculations are attached and compared to the values provided in the RASPA documentation. Any insight or explanation for the discrepancy would be appreciated!

RASPA Ammonia Synthesis Partition Function.pdf

Creating molecules for more systems than the maximum allowed: 1

Dear developers,

I often find the following error message when I use RASPA 2.0.48:
Creating molecules for more systems than the maximum allowed: 1

There was no other information, so it's hard to locate the where is the problem, input script or input cif file?
The following are input files that can reproduce this error:
raspa_input.zip

My system is Unbuntu 22.04

Missing molecules/* files ?

The commit 08c21c8 [Updated examples] deleted all the molecule files for all the directories in molecules/ (except for the ExampleDefinitions directory. So there is no longer TraPPE, TraPPE-EH, TraPPE-UA, CastilloVlugtCalero2009, or EPM2 molecule definitions. The Makefiles are still there. I can work around this (we have used these definitions in the past for automated tests to make sure our RASPA build or other dependent code is working), but I wanted to see if this was intentional or an accident...? Thanks!!

Partition function for propene

In the RASPA2 manual, https://raw.githubusercontent.com/numat/RASPA2/master/Docs/raspa.pdf

page 106,

ExternalTemperature 450.0

ExternalPressure 101300.

...

MoleculeName propene

LnPartitionFunction 87.1384

In version 2.0.37 manual, page 106

PartitionFunction 6.977909e37

looks to me the LnPartitionFunction was obtained by taking natural log on the previous version (exp(87.1384)~ 6.97...e37)

However, if I compare

https://github.com/numat/RASPA2/blob/master/examples/Tutorial/ReactionEnsembleAmmonia/simulation.input

N2

LnPartitionFunction 208.188

In version 2.0.37, examples/Tutorial/ReactionEnsembleAmmonia/simulation.input

N2 is

PartitionFunction 3.81253e4

that is not associated with exp, namely exp(208.188) >> 3.8..e4

I think in the N2 example, the atomization energy was used in the new partition function after version 2.0.37. (https://github.com/iRASPA/RASPA2/blob/master/ChangeLog.md, "Updated partition factors for ReactionEnsembleAmmonia example")

With/without atomization energies (from https://cccbdb.nist.gov/atomize2.asp, Propene about 3395 kJ/mol experimental atomization energies), I cannot obtain the 6.977909e37 for propene.

May I know how the propene partition function value was obtained? Thank you very much (reposted from the raspa2 forum https://forums.iraspa.org/index.php?topic=1247.0 )

RASPA for a database

Hi everyone,

I have a question about using RASPA for a large number of MOFs. How could we calculate the adsorption of gas in a large number of MOFs? in many scientific papers, the authors have reported the calculation of gas adsorption in a large number of MOFs using RASPA. how long does it take?

Thanks!

Trouble running RASPA simulation

Hi,
I managed to compile and install the program using the pdf manual and comments under some of the other issues on here.
I copied the run file from the Methane in a Box example into my simulations/bin folder. When I do ./run in bash I get an error message as below:
mynameandcomputer:~/RASPA/RASPA2/simulations/bin$ ./run
Shift all potentials
'force_field.def' file not found and therefore not used

(When downloading the code I put it in the RASPA folder, and RASPA2 is a sub-folder, I took this into account when tinkering with stuff so I thought it was okay, but I could be wrong.)

Thanks.

Documentation - pdf manual

Dear Raspa developers,

thank you very much for the great work you are doing! I have a few questions and suggestions related to the documentation of your project.

1. I was not able to find the raspa.pdf manual in the current github repository. The newest version I was able to find is from numat / RASPA2 and it is from 27th January 2020. All my notes will be with respect to that version. It would be nice if the raspa.pdf file is added to the Docs directory.

2. In section 1.2 Units and conventions would be desirable to briefly mention the minimum image convention, as it has a consequences for the size of simulation cell. (Example 6 is dealing with minimum image convention, but prior to that example, there is no sign of cell-size limitations)

3. In section 2.1 a zframework.def file is mentioned. However, I was not able to find any example of such file. It is evident that it would be similar to the molecule.def file, but some differences must be present (e.g., no critical constants).

4. During the study of Examples, I have found some settings not mentioned in the 2.2 Simulation input section:
   ComputeNumberOfMoleculesHistogram
   WriteNumberOfMoleculesHistogramEvery
   NumberOfMoleculesHistogramSize
   NumberOfMoleculesRange
   ProbabilityCFCRXMCLambdaChangeMove (and the related setting for Components)

5. In Non-basic example 1 I believe I found an error. Component 1 should have IdentityChangesList 1 0 instead of 0 1

6. In Non-basic example 3, I was confused how the box was filled with water molecules, even though the CreateNumberOfMolecules is 0. Some explanation may be desirable (at least for users like me).

7. Is Raspa using IdealGasRosenbluthWeight and IdealRosenbluthValue (Basic Example 7)? Is there any difference between these two?

I do apologize for this long list of comments and questions. I am sending it in hope that such notes may help make the manual more clear for users.

Thank you and have a nice day!
Michal T.

p_1 of MORSE2* potentials should be labeled as unitless

I think this involves potentials.c, output.c and Docs/Potentials/potentials.tex.
Based on what potentials.c (lines 6250, 6262, 6280) shows, the following lines should have [A^-1] changed to [-]:

• potentials.c lines 6242, 6256, 6274, 7735, 7749, 7772, 9547, 9563, 9590, 11149, 11480
• output.c lines 2779, 2782, 2796, 2798, 2809, 2811
• potentials.tex line 841

Other versions of Morse are fine - just Morse2.

Potential bug installing RASPA in Ubuntu 20.10

Hi, I was installing RASPA2 in my Ubuntu 20.10, everything worked fine but as a i tried to compile via make i got the an error indicating that <sys/systctl.h> was missing. From my understanding, the systctl.h is in the linux folder. I changed the location and it compiled everything successfully.

I don't know if this is a bug or if I did something wrong. I just let this issue open in case you guys have a clue about this point.

Installation not working with Intel

I'm trying to compile RASPA2 using Intel 20.0.4 in an HPC cluster, however, I get some errors when intel get statistics.c at line 3417.
It gets me something like this

...

/bin/sh ../libtool --tag=CC   --mode=compile icc -DPACKAGE_NAME=\"RASPA\" -DPACKAGE_TARNAME=\"raspa\" -DPACKAGE_VERSION=\"2.0\" -DPACKAGE_STRING=\"RASPA\ 2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"raspa\" -DVERSION=\"2.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_MATH_H=1 -DHAVE_STRING_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I.     -Wall -fast -MT statistics.lo -MD -MP -MF .deps/statistics.Tpo -c -o statistics.lo statistics.c
libtool: compile:  icc -DPACKAGE_NAME=\"RASPA\" -DPACKAGE_TARNAME=\"raspa\" -DPACKAGE_VERSION=\"2.0\" "-DPACKAGE_STRING=\"RASPA 2.0\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"raspa\" -DVERSION=\"2.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_MATH_H=1 -DHAVE_STRING_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -Wall -fast -MT statistics.lo -MD -MP -MF .deps/statistics.Tpo -c statistics.c  -fPIC -DPIC -o .libs/statistics.o
statistics.c(3417): error: expected an expression
    for(int i=0;i<NR_BLOCKS;i++)
        ^

statistics.c(3417): error: identifier "i" is undefined
    for(int i=0;i<NR_BLOCKS;i++)
                ^

statistics.c(3442): error: expected an expression
        for(int i=0;i<NR_BLOCKS;i++)
            ^

statistics.c(3468): error: expected an expression
        for(int i=0;i<NR_BLOCKS;i++)

...

I'm using the instructions provided in README.md in a script to configure the makefile as follows:

#!/bin/sh

module load intel/20.0.4 qt/4.8.7_intel-2017_update-1

rm -rf autom4te.cache
mkdir m4
aclocal
autoreconf -i
automake --add-missing
autoconf

rm config.cache
export CFLAGS="-Wall -fast"
export CC="icc"
./configure --prefix=${HOME}/iRASPA2/icc

Complete log file: make_RASPA2.log

Molecular trajectories during MSD simulation

Hi, I want to calculate the diffusion of a molecule through a MOF system. I am wondering if there is option to get the trajectory of the molecule component during the MD simulation process. I tried to look for the coordinates of the molecule but couldn't find it.

Problems in RASPA2 installation

Typo in conversion factor

The line of the output

Conversion factor molecules/unit cell -> gr/gr:       x.xxxxxxxxx [-]

should read instead:

Conversion factor molecules/unit cell -> mg/g:       x.xxxxxxxxx [-]

Indeed, in the final section where Average loading are reported, this factor is used but with the correct units:

Average loading absolute [milligram/gram framework]         xx.xxxxxxx +/-

To avoid problems in back compatibility (probably many users already noticed this problem and corrected their parser) I suggest to replace the label to mg/g instead of dividing the value by 1000, so that the users are forced to update their parser instead of suddently have a different value.

Error opening input-file

Hello, I'm completely new to RASPA but really hoping to learn how to use it.
I'm having a bit of an issue on mac, I managed to install raspa2 through conda forge however when I run 'simulation -i' it gives me the following error. I was hoping someone could help me understand how to fix this, thank you!

Error opening input-file 'simulation.input' (routine int LoadFile(char *path))
zsh:` segmentation fault simulate i

Average Widom Rosenbluth factor for quartz

I'm getting an average widom weight of around 3e-24 for quartz framework. I'm not sure why it is showing this low value although quartz has significant pores in it. Would highly appreciate your help. Thanks

memory leaks?

I just ran cppcheck over the code.

While most notes are about uninitialized variables (maybe good to fix, but not necessarily relevant), it also came up with two memory leaks that are probably good to investigate/close:

src/minimization.c:5443:1: error: Memory leak: Gradient [memleak]
}
^
src/minimization.c:5443:1: error: Memory leak: EigenValues [memleak]
}
^

Furthermore there were a couple of those:

src/ewald.c:471:3: error: Common realloc mistake: 'Positions' nulled but not freed upon failure [memleakOnRealloc]
  Positions=(VECTOR*)realloc(Positions,MaxNumberOfCoulombicSites*sizeof(VECTOR));
  ^

Full output: cpp-check.txt

zif 11 and zif 12 structures identical

Just noticed in passing that the structures of zif 11 and 12 in https://github.com/iRASPA/RASPA2/tree/master/structures/mofs/cif are identical (I guess one of them is wrong)

Not important, just to keep track of this

The critical temperature, the critical pressure, and the acentric factor of water in TIP5P.def are data of CO2

The critical temperature, the critical pressure, and the acentric factor of water in TIP5P.def are data of CO2

Issue with Ethene adsorption calculations in MOF

Hi,

I have been doing ethene adsorption calculations in MOFs. The adsorption amount and heat of adsorption values were not matching with the experimental values. The results are very low (almost 10 times) compared to experiments. To check the forcefield of the framework and guest, i have applied different guests in the framework. I got the results close to the literature, unlike ethene. I guess something is not correct with ethene. What are the files I should look after in case the guest molecule causing an issue?
I have attached the force_field.def and simulation.input files. Please let me know what could be the possible reason?

Thank you.
ethene in ZIF-8.zip

commmand not found

I used the raspa guides and instal the program, but when I want to run the raspa examples for testing the program I received this error: "command not found"
In below I mentioned the code that I used:

simulate simulation.input

I really appreciate any help you can provide
Best regard

Installation Issue

Hi, I was trying to install the latest RASPA2 but it refuses to compile with some linker problem with the errors like below:
/bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O3 -mfpmath=sse -fomit-frame-pointer -ftree-vectorize -fno-stack-check -funroll-loops -ffast-math -o simulate main.o libraspa2.la libtool: link: gcc -Wall -O3 -mfpmath=sse -fomit-frame-pointer -ftree-vectorize -fno-stack-check -funroll-loops -ffast-math -o .libs/simulate main.o ./.libs/libraspa2.so -lm -Wl,-rpath -Wl,/home/ekn8665/RASPA/simulations/lib ./.libs/libraspa2.so: undefined reference to HybridNVEAlchDrift'`
Wondering how to get it fixed.
Thanks!

Visualization with raspa2.0

Hello everyone!

I have been performing hydrogen adsorption simulations on MOFs for some time. but since then I have faced the visualization problem. the RASPA tutorial says that we can visualize the density and even the molecules with vtk but I still can't. I simulate RASPA2.0 on my PC with a Linux environment. I need your help, please.

Installation

I am trying to install the package locally follow the instruction here, but couldn't find any of these files.
• rm -rf autom4te.cache
• mkdir m4
• aclocal
• autoreconf -i
• automake --add-missing
• autoconf
• ./configure --prefix=${RASPA_DIR}
There is also no configure file in any directory. Am I doing it right?

FEYNMAN HIBBS LENNARD JONES

what is the mixrule when i use FEYNMAN HIBBS LENNARD JONES to calculate E/P?
The manual says :Jorgensen or Lorentz-Berthelot only used for Lennard-Jones

Warning in Raspa simulation

I am currently running an adsorption isotherm simulation for N2 in CuBTC.
I end up getting this warning in the output.

My previous simulations have been alright. I am not able to figure out this warning, aslo the Iraspa community

WARNING: THERE ARE ATOM-PAIRS WITH NO VDW INTERACTION N_n2-N_com N_n2-Cu1 N_n2-O1 N_n2-C1 N_n2-C2 N_n2-C3 N_n2-H1 N_com-N_n2 N_com-Cu1 N_com-O1 N_com-C1 N_com-C2 N_com-C3 N_com-H1 Cu1-N_n2 Cu1-N_com Cu1-O1 Cu1-C1 Cu1-C2 Cu1-C3 Cu1-H1 O1-N_n2 O1-N_com O1-Cu1 O1-C1 O1-C2 O1-C3 O1-H1 C1-N_n2 C1-N_com C1-Cu1 C1-O1 C1-C2 C1-C3 C1-H1 C2-N_n2 C2-N_com C2-Cu1 C2-O1 C2-C1 C2-C3 C2-H1 C3-N_n2 C3-N_com C3-Cu1 C3-O1 C3-C1 C3-C2 C3-H1 H1-N_n2 (maximum 50 interactions shown)
WARNING: ENERGY DRIFT (INTERNAL CONSISTENCY ERROR IN THE CODE), THE SIMULATION RESULTS ARE WRONG!! isn't loading.

Installation

I tried to install RASPA2 using several recommended ways. But nothing seems to be working for me. Can anyone help me with the step-by-step process? I tried both the documentation and the readme file.