You have:

###Command Line

which does not render correctly. You need to have:

### Command Line

Similarly for some of your other headers.

Hi. I am simulating a CO2 adsorption isotherm and I'd like RASPA to pull the charges from the .cif, which are different from every atom. So, following the manual, I put in my simulation.input file:

UseChargesFromCIFFile yes
RemoveAtomNumberCodeFromLabel yes

Using the following .cif file, I do not get a seg fault and RASPA reads the charges appropriately.

data_KAXQIL-clean_labeled

_cell_length_a 5.567300
_cell_length_b 11.821400
_cell_length_c 22.760300
_cell_angle_alpha 100.355998
_cell_angle_beta 90.000000
_cell_angle_gamma 90.000000
_cell_volume 1473.528419

_symmetry_space_group_name_H-M   'P 1'
_symmetry_Int_Tables_number 1

loop_
_symmetry_equiv_pos_as_xyz
 'x, y, z'

loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_charge
Ca1 Ca 0.755850 0.636820 0.722870 1.0
H1 H 0.199600 0.194500 0.618900 1.0
C1 C 0.741400 0.004540 0.734890 0.0
S1 S 0.963630 0.398350 0.607680 -1.0
O1 O 0.805000 0.493100 0.630960 -1.0

However, when I use the exact same .cif file, except adding more atoms to the end, I receive a seg fault. Why would the seg fault depend on the number of atoms in the .cif file? Is there a limit to how many different atoms e.g. O12 that we can label differently? Thanks. Below is the .cif file that yields a seg fault.

UPDATE The seg fault goes away when I change the simulation.input to read:

UseChargesFromCIFFile no

and instead put charges in the pseudo_atoms.def file.

data_KAXQIL-clean_labeled

_cell_length_a 5.567300
_cell_length_b 11.821400
_cell_length_c 22.760300
_cell_angle_alpha 100.355998
_cell_angle_beta 90.000000
_cell_angle_gamma 90.000000
_cell_volume 1473.528419

_symmetry_space_group_name_H-M   'P 1'
_symmetry_Int_Tables_number 1

loop_
_symmetry_equiv_pos_as_xyz
 'x, y, z'

loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_charge
Ca1 Ca 0.755850 0.636820 0.722870 1.593783
Ca2 Ca 0.255850 0.863180 0.777130 1.593776
Ca3 Ca 0.244150 0.363180 0.277130 1.593783
Ca4 Ca 0.744150 0.136820 0.222870 1.593776
H1 H 0.199600 0.194500 0.618900 0.099731
H2 H 0.124900 0.231800 0.406100 0.115298
H3 H 0.554100 0.420600 0.537200 0.098276
H4 H 0.562300 0.338800 0.672900 0.102220
H5 H 0.478300 0.183900 0.719700 0.086178
H6 H 0.118600 0.043900 0.669100 0.107920
H7 H 0.206600 0.275100 0.507800 0.099698
H8 H 0.471300 0.373100 0.435800 0.094271
H9 H 0.699600 0.305500 0.881100 0.099731
H10 H 0.624900 0.268200 0.093900 0.115298
H11 H 0.054100 0.079400 0.962800 0.098276
H12 H 0.062300 0.161200 0.827100 0.102220
H13 H 0.978300 0.316100 0.780300 0.086178
H14 H 0.618600 0.456100 0.830900 0.107920
H15 H 0.706600 0.224900 0.992200 0.099698
H16 H 0.971300 0.126900 0.064200 0.094271
H17 H 0.800400 0.805500 0.381100 0.099731
H18 H 0.875100 0.768200 0.593900 0.115298
H19 H 0.445900 0.579400 0.462800 0.098276
H20 H 0.437700 0.661200 0.327100 0.102220
H21 H 0.521700 0.816100 0.280300 0.086178
H22 H 0.881400 0.956100 0.330900 0.107920
H23 H 0.793400 0.724900 0.492200 0.099698
H24 H 0.528700 0.626900 0.564200 0.094271
H25 H 0.300400 0.694500 0.118900 0.099731
H26 H 0.375100 0.731800 0.906100 0.115298
H27 H 0.945900 0.920600 0.037200 0.098276
H28 H 0.937700 0.838800 0.172900 0.102220
H29 H 0.021700 0.683900 0.219700 0.086178
H30 H 0.381400 0.543900 0.169100 0.107920
H31 H 0.293400 0.775100 0.007800 0.099698
H32 H 0.028700 0.873100 0.935800 0.094271
C1 C 0.741400 0.004540 0.734890 0.770321
C2 C 0.739300 0.276740 0.344930 0.753881
C3 C 0.890800 0.355060 0.531360 -0.212544
C4 C 0.889600 0.281060 0.642190 -0.226848
C5 C 0.056700 0.192960 0.639960 -0.035051
C6 C 0.011400 0.270250 0.432280 -0.051244
C7 C 0.792700 0.301280 0.410690 -0.111260
C8 C 0.668700 0.383440 0.510800 -0.030029
C9 C 0.672800 0.279490 0.671900 -0.016710
C10 C 0.624400 0.187240 0.700250 -0.049265
C11 C 0.007100 0.102620 0.669600 -0.058585
C12 C 0.061000 0.296550 0.493050 -0.037486
C13 C 0.791700 0.099820 0.699940 -0.108435
C14 C 0.620400 0.355460 0.450210 -0.036560
C15 C 0.241400 0.495460 0.765110 0.770321
C16 C 0.239300 0.223260 0.155070 0.753880
C17 C 0.390800 0.144940 0.968640 -0.212544
C18 C 0.389600 0.218940 0.857810 -0.226848
C19 C 0.556700 0.307040 0.860040 -0.035051
C20 C 0.511400 0.229750 0.067720 -0.051244
C21 C 0.292700 0.198720 0.089310 -0.111260
C22 C 0.168700 0.116560 0.989200 -0.030029
C23 C 0.172800 0.220510 0.828100 -0.016710
C24 C 0.124400 0.312760 0.799750 -0.049265
C25 C 0.507100 0.397380 0.830400 -0.058585
C26 C 0.561000 0.203450 0.006950 -0.037486
C27 C 0.291700 0.400180 0.800060 -0.108435
C28 C 0.120400 0.144540 0.049790 -0.036560
C29 C 0.258600 0.995460 0.265110 0.770321
C30 C 0.260700 0.723260 0.655070 0.753881
C31 C 0.109200 0.644940 0.468640 -0.212544
C32 C 0.110400 0.718940 0.357810 -0.226848
C33 C 0.943300 0.807040 0.360040 -0.035051
C34 C 0.988600 0.729750 0.567720 -0.051244
C35 C 0.207300 0.698720 0.589310 -0.111260
C36 C 0.331300 0.616560 0.489200 -0.030030
C37 C 0.327200 0.720510 0.328100 -0.016710
C38 C 0.375600 0.812760 0.299750 -0.049265
C39 C 0.992900 0.897380 0.330400 -0.058585
C40 C 0.939000 0.703450 0.506950 -0.037486
C41 C 0.208300 0.900180 0.300060 -0.108435
C42 C 0.379600 0.644540 0.549790 -0.036560
C43 C 0.758600 0.504540 0.234890 0.770321
C44 C 0.760700 0.776740 0.844930 0.753881
C45 C 0.609200 0.855060 0.031360 -0.212544
C46 C 0.610400 0.781060 0.142190 -0.226848
C47 C 0.443300 0.692960 0.139960 -0.035051
C48 C 0.488600 0.770250 0.932280 -0.051244
C49 C 0.707300 0.801280 0.910690 -0.111260
C50 C 0.831300 0.883440 0.010800 -0.030030
C51 C 0.827200 0.779490 0.171900 -0.016710
C52 C 0.875600 0.687240 0.200250 -0.049265
C53 C 0.492900 0.602620 0.169600 -0.058585
C54 C 0.439000 0.796550 0.993050 -0.037486
C55 C 0.708300 0.599820 0.199940 -0.108435
C56 C 0.879600 0.855460 0.950210 -0.036560
S1 S 0.963630 0.398350 0.607680 1.152829
S2 S 0.463630 0.101650 0.892320 1.152829
S3 S 0.036370 0.601650 0.392320 1.152829
S4 S 0.536370 0.898350 0.107680 1.152829
O1 O 0.805000 0.493100 0.630960 -0.623849
O2 O 0.915200 0.262260 0.309360 -0.784012
O3 O 0.218900 0.415340 0.611760 -0.532385
O4 O 0.525700 0.984230 0.743780 -0.735465
O5 O 0.919100 0.956950 0.752850 -0.713610
O6 O 0.525100 0.267580 0.328320 -0.711065
O7 O 0.305000 0.006900 0.869040 -0.623848
O8 O 0.415200 0.237740 0.190640 -0.784011
O9 O 0.718900 0.084660 0.888240 -0.532385
O10 O 0.025700 0.515770 0.756220 -0.735465
O11 O 0.419100 0.543050 0.747150 -0.713610
O12 O 0.025100 0.232420 0.171680 -0.711065
O13 O 0.195000 0.506900 0.369040 -0.623849
O14 O 0.084800 0.737740 0.690640 -0.784012
O15 O 0.781100 0.584660 0.388240 -0.532385
O16 O 0.474300 0.015770 0.256220 -0.735465
O17 O 0.080900 0.043050 0.247150 -0.713610
O18 O 0.474900 0.732420 0.671680 -0.711065
O19 O 0.695000 0.993100 0.130960 -0.623848
O20 O 0.584800 0.762260 0.809360 -0.784012
O21 O 0.281100 0.915340 0.111760 -0.532385
O22 O 0.974300 0.484230 0.243780 -0.735465
O23 O 0.580900 0.456950 0.252850 -0.713611
O24 O 0.974900 0.767580 0.828320 -0.711065

From this conversation, process.join() is behaving differently on different UNIX OS's.

The underlying reason for this should be researched. If needed, OS-specific join commands should be used.

Hi,

does this distribution of RASPA2 support energy-bias insertion for Monte Carlo as it is described e.g. in
this paper ? (Is there any version availible, that supports this type of moves?)

Thank you,
Alex

Highly cited stack overflow here.

The code uses a pattern like

Framework[system].ExclusionMatrix[f1]=(char**)calloc(largest_size,sizeof(char*));

Stop this unless absolutely necessary.

I'm attempting to run a basic simulation in NVT ensemble, so I was running:

Basic/MC_Methane_in_Box

When I change the line:

CreateNumberOfMolecules 100

...to:

CreateNumberOfMolecules 128

It still only runs with 100 molecules in the box. I wasn't able to find any info in the manual explaining this behavior to me. Can you please explain why it's not using the number I specified?

Hi, This is Joyjit. I'm a new user of RASPA and facing the following issue. RASPA does not give any output when the volume fraction of an adsorbate is high enough in case of NVT simulations. Example-

SimulationType MonteCarlo
NumberOfCycles 200
NumberOfInitializationCycles 0
PrintEvery 10

Forcefield GarciaPerez2006

Box 0
BoxLengths 25 25 25
ExternalTemperature 120.0
Movies yes
WriteMoviesEvery 10

Component 0 MoleculeName decane
MoleculeDefinition TraPPE
TranslationProbability 1.0
RotationProbability 1.0
RegrowProbability 1.0
ReinsertionProbability 1.0
SwapProbability 0.0

CreateNumberOfMolecules 100

I do not see any output when I run the above simulation. But, when I set "CreateNumberOfMolecules 50", I get the usual outputs. One can also see similar effect by changing the "BoxLengths". In case of MOFs also, I see similar issues. I believe that these numbers of host molecules are quite low compared to the capacity of a box or a MOF. Any idea or resolution?

Hello all.
I am a beginner to RASPA package. I tried running structure.cif file in python but its showing some error. So how I can convert it to P1 symmetry cif file as mentioned in the below link-
https://github.com/numat/RASPA2/wiki/Workflow
Since Material studio is not an open source, can somebody tell me another way?
I am doing the calculation in linux using normal computer.

Thanks,

Hello,
I use RASPA2 for simulations of hydrogen adsorption by MOFs.I wanted to use some MOFs like IRMOF-20, SNU-70, UMCM-9, NU-100, MOF-74, HKUST-1, and many others. My concern is that these materials are not in the cif file of RASPA2. How can I do ?
My regards!
 

hello guys, I want to learn running RASPA using python, but I fail with the example given in the git(as follow). actually, I can't figure out the ''run'' function defined in raspa2.py "def run(structure, molecule_name, temperature=273.15, pressure=101325,
helium_void_fraction=1.0, unit_cells=(1, 1, 1),
framework_name="streamed", simulation_type="MonteCarlo", cycles=2000,
init_cycles="auto", forcefield="CrystalGenerator",
input_file_type="cif")"
which one should be the input parameter "structure" in function run.
If I just want to test one material ''Cu-BTC.cif'', how should I make it with "run" function.

thanks!

import RASPA2

Set up

gas = "CO2"
pressures = [1e4 * 10**(0.1 * i) for i in range(21)]

Run

results = [RASPA2.run(my_structure, gas, temperature=298, pressure=pressure)
for pressure in pressures]

Parse

uptakes = [r["Number of molecules"][gas]
["Average loading absolute [cm^3 (STP)/cm^3 framework]"][0]
for r in results]

Plot

plot(pressures, uptakes)

Hello,
I took the cif file of MOF-200 and MOF-177 from RASPA which I then doped with transition metals using Gausvew and Avogadro to increase the interactions during adsorption of the hydrogen. But I can't simulate the adsorption of hydrogen by the cif file of doped MOF / how to do it please.

Issue by patrickfuller
Wednesday Aug 21, 2013 at 21:35 GMT
Originally opened as https://github.com/numat/RASPA/issues/10

In order to stream data, the current logic uses fmemopen and open_memstream. These are POSIX-only commands, and not supported on macs.

Look into a cross-platform solution.

Issue by patrickfuller
Friday Jul 26, 2013 at 16:16 GMT
Originally opened as https://github.com/numat/RASPA/issues/1

From the source. I can't comment on these personally, but they look important.

URGENT

5. CIF-reader: handle occupancy<1

6. pressure/stress in SHAKE

7. bond-information in CIF-file

8. _data in CIF-file (e.g. several section of _atom_site)

9. BornTerm (correction for rigid units)

10. second-derivative for bend-rigid and torsion-rigid flexible-rigid transitions

11. modify Buckingham, to avoid overlap

12. document potentials

13. check dielectric constant

14. check growing without bending/torsion

15. strain-derivative anisotropic model

SPECIFIC

1. ring topologies using CBMC
2. analytical expression for Born-terms
3. correct 3D density-plots for framework drift
4. remove kinetic energy from core-shell pair (see Rattle)
5. finish direct Coulomb, shifted Coulomb, Wolf-method, molecular cutoff
6. analytical expressions for cross-terms (bond/bend, bond/torsion, bend/bend, bend/torsion, etc)
   Hessian, Born term, and cross terms for all potentials

GENERAL

speed optimization
Monte-Carlo routines for bond-dipoles
Minimization using constraints
cyclic flexible molecules
symplectic NosePointCare integrators for NVT, NPT, and NPT-PR
Documentation
Verify code with test-cases
Make Examples
Reptation move
Verlet lists/ cell lists
symmetry/spacegroup for force/hessian
all inverse space groups
find space group(s)
saddle point search
VDW using Ewald
Histogram-reweighting (run-time)
Ewald 2D
Add clays, carbon-nanotubes, and metal-oxides structures
Lattice Boltzmann
Lattice gases
Kinetic Monte Carlo
Graphical User Interface (QT, Cocoa)

Hello i am new to RASPA2. I would like to know if there is a way to get the molecules position x.y.z of my simulations ?

Error: no energy conservation in internal MC scheme (Bend 301.828353)
This error message only shows up when a 5 united carbon chain is used.
C6 and C7 is fine. What's wrong with C5? I checked the mol files. There is nothing wrong there.

SimulationType MonteCarlo
NumberOfCycles 100
NumberOfInitializationCycles 1
PrintEvery 1

Forcefield GenericMOFs
CutOffVDW 10.0
Box 0
BoxLengths 26 26 26
BoxAngles 90 90 90
ExternalTemperature 298

Component 0 MoleculeName C5
MoleculeDefinition TraPPE
IdealGasRosenbluthWeight 0.021348
TranslationProbability 1.0
RotationProbability 1.0
ReinsertionProbability 1.0
CBMCProbability 1.0
CreateNumberOfMolecules 4

Dear All,
I could not find the forcefield parametre for carbon monoxide, CO.def file in RASPA directory. I wanted to do a simulation with carbon monoxide gas. How can I get the '.def' file for CO.
Thanks

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

Hi everyone,

I am using RASPA2 without any problem from the command line (simulate sim_isotherme.input) but I am having trouble lauching it from IPython Notebook. Being in the right directory, the following commands do not produce any result or error (the program is just running empty) :
import RASPA2
RASPA2.run_script("sim_isotherme.input", structure=None, stream=True)

Can anybody help? Thank you very much!

These things are a nightmare to free.

Example:

SpectrumPseudoAtoms=(REAL *****)calloc(NumberOfSystems,sizeof(REAL****));

The framework net charge is not zero when the charges are read from a CIF file. (e.g. -2.55e-13) I verified that the atomic charges sum to zero. Same problem when I put the charges in the force field file.

It only happens when Ewald is used for electrostatics.

I installed RASPA using pip. I will try to compile it from scratch to see if I still have the same problem.

Dear person to whom it may concern:

As a test for GCMC simulations of RASPA2, I performed N2 adsorption simulations in ZIF-8 at 77K at varied pressures.
The results were not what I expected because the N2 adsorption amounts for given pressures ( 0.2 - 5000 Pa) were extremely high.
Cap anyone help me with this?

Best regards,

(e.g., 62
output.txt
0 mol/kg at 1 Pa).

Issue by patrickfuller
Friday Jul 26, 2013 at 16:18 GMT
Originally opened as https://github.com/numat/RASPA/issues/2

1. Compilation should not raise warnings.
2. Valgrind should run pure. No memory leaks!
3. Look into static analysis + linting for C (I've never done it before, but cppcheck looks promising).
4. Reduce the dependency on globals.

Hi,
I'm trying to do a simulation in which the adsorbate is polarized and there is an external electric field acting on it. Is this implemented in RASPA? If not, where do you need to modify the code to do that?

it there any information to show raspa2 installed with fftw3, blas and lapack?
during the configure process, it prints out
"checking for library containing ddot_... -lblas
checking for library containing dsyevd_... no
checking for library containing fftw_plan_dft_r2c_1d... -lfftw3
"
Are these showing whether the fftw3, blas, lapack can be used by raspa2?
But even if there is the library file of lapack ( liblapack.a ), the result of checking dsyevd is still "no".
Is it normal? or someone tells me something about this?

Thank you very much

Respected Sir, I am new user of RASPA, when I am starting a simulation the following error is showing, kindly tell me how to overcome this problem.

WARNING: THERE ARE ATOM-PAIRS WITH NO VDW INTERACTION ......

Thanking You

Regards
Biswajit

The scope of the other issues calls into question the overall architecture of this program. Namely, RASPA should 1. have an API and 2. be thread safe (no segfaults!).

The existing usage method of input/output files should be decoupled from the core logic and instead use a programmatic API.

API methods should be minimalist. Sensible defaults for every parameter, output minimum information unless specifically asked for.

In [1]: import this
The Zen of Python, by Tim Peters

Beautiful is better than ugly.
Explicit is better than implicit.
Simple is better than complex.
Complex is better than complicated.
Flat is better than nested.
Sparse is better than dense.
Readability counts.
Special cases aren't special enough to break the rules.
Although practicality beats purity.
Errors should never pass silently.
Unless explicitly silenced.
In the face of ambiguity, refuse the temptation to guess.
There should be one-- and preferably only one --obvious way to do it.
Although that way may not be obvious at first unless you're Dutch.
Now is better than never.
Although never is often better than *right* now.
If the implementation is hard to explain, it's a bad idea.
If the implementation is easy to explain, it may be a good idea.
Namespaces are one honking great idea -- let's do more of those!

Hello,

I would like to verify computation results programatically, e.g. given the example workflow:

...
# Distribute the jobs on the amazon cloud cores. Wait for the jobs to finish.
import cloud
jids = cloud.map(f, mofs)
uptakes = cloud.result(mofs)
# Verify the results:
for input, output in zip(mofs, uptakes):
    RASPA.verify(input, output)
...

Is there a trivial (computationally non-intensive) way to verify the results against given input?

Hi,
I would like to determine the heat of adsorption with RASPA2. I use the formula of the document but I do not get away because I have the pain to find , and .
and I also find this communication "#30" according to which RASPA increased the heat of adsorption. how to do it please?

Hello,
I am a new one who just installed RASPA2 for the simulation of hydrogen adsorption by MOFs. but when I want to run the simulation through the command lines we see the following eureur message:
gustave@gustave-HP-500B-Microtower:$ export RASPA_DIR=${HOME}/Research/simulations
gustave@gustave-HP-500B-Microtower:$ $RASPA_DIR/bin/simulate
Error opening input-file 'simulation.input' (routine int LoadFile(char *path))
Erreur de segmentation (core dumped)

and when I go through python I get the following eureur message:

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

will anyone please help me?
my regards !

Dear all
Where cn I find cif files for MIL-100 and MIL-101 with symmetry??
Thanks a lot
Dearly
lorenzo

Hi all,

I am trying to do GCMC Simulation for predicting adsorption behavior of CO2 in ZSM-5 (Si/Al=47).
For this purpose I used, Translation, Rotation, Reinsertion, and Swap moves, but in the output file it is showing that the initialization and production ensemble is NVE? Can anybody tell me why it does that?

Also, the charges provided in Garcia-Perez forcefield for Si, Al, H, and O give the framework a net charge of -0.6, So can I use +0.3 for the two hydrogens in my framework to make it electroneutral?

Hello everyon,

I am new to RASPA. I want to have chemical potential vs density using GCMC. But I don't know how to set the chemical potential as a constant in RASPA2. How can I do?

My regards!

Issue by patrickfuller
Monday Jul 29, 2013 at 00:31 GMT
Originally opened as https://github.com/numat/RASPA/issues/5

It's hard to debug RASPA + Monte Carlo because of the stochastic nature of the MC simulations. A test suite + deterministic tests would be nice.

Hi,

I'm about to purchase new sever for running RASPA 2,
but could RASPA 2 utilizes GPU in the computer?

Nvidia provides the performance enhancement data for various molercular simulation tools but
there is no test for RASPA.
https://www.nvidia.com/object/computational_chemistry.html

Seo-Yul Kim
Chemical engineering, Yonsei university

The N_n2 atom type VDW can be grid correctly. But I can not get the Ewald grid. The program will stop without any error.
I chekced the 'grid.c' code, but I can not figure out why the program halts.

Is there a N2 grid example available ?

Hello
I have just installed RASPA2 for hydrogen adsorption simulations in MOFs. I wanted to use some MOFs like IRMOF-20, SNU-70, UMCM-9, HKUST-1 and the NU-100. but I do not find it in the database. how should I do it?

How to get a Forcefield of a flexible MOFs like Dubbeldam2007FlexibleIRMOF-1? Or just use genericMOFs Forcefield

I'm attempting to compile the code. I get the following error:

gcc -pthread -shared -Wl,-z,relro build/temp.linux-x86_64-2.7/src/internal_born.o build/temp.linux-x86_64-2.7/src/framework_born.o build/temp.linux-x86_64-2.7/src/complex.o build/temp.linux-x86_64-2.7/src/minimization_simulation.o build/temp.linux-x86_64-2.7/src/molecule.o build/temp.linux-x86_64-2.7/src/linear_equations.o build/temp.linux-x86_64-2.7/src/simulation.o build/temp.linux-x86_64-2.7/src/utils.o build/temp.linux-x86_64-2.7/src/inter_born.o build/temp.linux-x86_64-2.7/src/thermo_baro_stats.o build/temp.linux-x86_64-2.7/src/movies.o build/temp.linux-x86_64-2.7/src/inter_force.o build/temp.linux-x86_64-2.7/src/molecular_dynamics.o build/temp.linux-x86_64-2.7/src/framework.o build/temp.linux-x86_64-2.7/src/scattering_factors.o build/temp.linux-x86_64-2.7/src/cbmc.o build/temp.linux-x86_64-2.7/src/vector.o build/temp.linux-x86_64-2.7/src/inter_hessian.o build/temp.linux-x86_64-2.7/src/rigid.o build/temp.linux-x86_64-2.7/src/cubic_spline_1d.o build/temp.linux-x86_64-2.7/src/internal_energy.o build/temp.linux-x86_64-2.7/src/main.o build/temp.linux-x86_64-2.7/src/input.o build/temp.linux-x86_64-2.7/src/inter_energy.o build/temp.linux-x86_64-2.7/src/framework_energy.o build/temp.linux-x86_64-2.7/src/charge_equilibration.o build/temp.linux-x86_64-2.7/src/molecule_properties.o build/temp.linux-x86_64-2.7/src/statistics.o build/temp.linux-x86_64-2.7/src/status.o build/temp.linux-x86_64-2.7/src/warnings.o build/temp.linux-x86_64-2.7/src/run.o build/temp.linux-x86_64-2.7/src/internal_hessian.o build/temp.linux-x86_64-2.7/src/spectra.o build/temp.linux-x86_64-2.7/src/minimization.o build/temp.linux-x86_64-2.7/src/potentials.o build/temp.linux-x86_64-2.7/src/framework_force.o build/temp.linux-x86_64-2.7/src/mc_moves.o build/temp.linux-x86_64-2.7/src/spacegroup.o build/temp.linux-x86_64-2.7/src/ewald.o build/temp.linux-x86_64-2.7/src/integrate.o build/temp.linux-x86_64-2.7/src/grids.o build/temp.linux-x86_64-2.7/src/internal_force.o build/temp.linux-x86_64-2.7/src/numerical.o build/temp.linux-x86_64-2.7/src/matrix.o build/temp.linux-x86_64-2.7/src/recrossing.o build/temp.linux-x86_64-2.7/src/equations_of_state.o build/temp.linux-x86_64-2.7/src/output.o build/temp.linux-x86_64-2.7/src/monte_carlo.o build/temp.linux-x86_64-2.7/src/integration.o build/temp.linux-x86_64-2.7/src/sample.o build/temp.linux-x86_64-2.7/src/framework_hessian.o build/temp.linux-x86_64-2.7/src/constants.o -L/usr/lib64 -lpython2.7 -o build/lib.linux-x86_64-2.7/RASPA2/simulations/lib/libraspa2.so
/bin/ld: cannot find -lpython2.7
collect2: error: ld returned 1 exit status
error: command 'gcc' failed with exit status 1

The error is strange as /usr/lib/ has the supposedly missing library python2.7 and /usr/lib is included in LD_LIBRARY_PATH. Not sure why the installation script might not be picking it up.... the bizarre part is the python2.7 lib module was used to retrieve the installer, so earlier in the installation chain it was clearly aware of the library.

I attempted to install with the command "pip install RASPA2", as directed in the README.

My distribution is : CentOS Linux release 7.1.150

Issue by TaeWonChoi
Wednesday Aug 07, 2013 at 15:31 GMT
Originally opened as https://github.com/numat/RASPA/issues/8

Current parser is not complete - few sections are skipped/ignored/overwritten
The parser focuses heavily on post-simulation data, instead of updates of simulation itself
These sections that are ignored, however, are either already recorded somewhere else, or unnecessary to record
For example, chunk of these data can be located through input files, mol files, forcefield etc.

• PSEUDO ATOM section

  Over-writes - only one value of Pseudo Atom is returned
  Check your forcefield - pseudo_atoms.def file have exact same data

• Current Box, Box-lengths , Box-angles

  In "[Init] Current cycle:...." and "Current cycle"
  Current Box, Box-lengths, Box-angles are jumbled up in one row or represented as a matrix

• Any "Performance...." key does not have good splitting pattern

  It still shows string values, but not organized

• "Current cycle: __ out of __" values

  They are all strings : none of them are in float
  You can view what values are, but not use it for further calculation

Can i compile RASPA2 with openmpi or mpich or on Intel Parallel Studio for parallel computation.

Hi guys and gals,
For many of you who may have a lot of questions, iRASPA forum is a better place to go.
You will get authentic answers from the authors and contributors of the code!
https://forums.iraspa.org/
Thanks!

Hi! I have been using RASPA2 for a while.
Recently I installed it on another Linux platform. When I simulate a MC job, it runs well except that there is no file created in the Output/System_0 directory. No matter what parameters I try, this bug persists.
How could I fix it? Thanks.

Seems like the forcefield description of water water.def in TraPPE forcefield folder is not entirely correct:

• The attempt to use it in simulations fails with the error:
  " Unknown group type (should be 'Flexible' or 'Rigid')"
• It is likely because in the file the number of atoms is defined BEFORE the group type (lines 10 and 11). Once they are swapped, the simulations work fine
• IDs of the bonds are messed up (on lines 18-19: 0 and 0 instead of 0 and 1, probably). Is it important?

Due to the fact that RASPA2 threw out all commit information before becoming 2, git can't be used to auto-merge this with the changes made in numat/RASPA.

I think the best way to merge these would be to manually make the changes required in a series of new commits. This includes:

• Streaming functionality
• Python bindings
• Printing out warnings and errors to stderr

Hi,

I'm trying to use this package for the simulation of CO2 adsorption on MOF on Windows with Python 3.5.1.

During the installation using the command : "pip install RASPA2 " I got some errors as you can see in the pdf file.
error_raspa.pdf

Did someone know this error and know how to fix it ? (therefore I don't get the "simulate" command)

Best regards

Sebastien Vaesen
Trinity College Dublin

This is a set of issues around running 100k+ simulations with RASPA, and stems mainly from its memory leaks. Currently, RASPA leaks a lot of memory, which builds up over many simulations. The "solution" currently used is to run every simulation in its own process, ie.

• Spin out new process
• Run simulation
• Shut down process, letting OS attempt to handle memory management

This logic really slows down high-throughput screening, and results in a lot of unexplained segmentation faults and generally not playing well with other programs. Instead, screening should use one process per core, and each core should be capable of running an unlimited number of simulations serially.

History of debugging this:

• libraspa shut down after 2-3 runs. This was due to a ridiculous amount of memory (~400 MB) leaking in movies.c. 72002b9 fixed this.
• libraspa shut down after 128 runs. This was due to 4 dangling file pointers per run and an OS limit of 512 file pointers per process (128 * 4 = 512). a659eba cleaned up dangling file pointers and removed this limit.
• libraspa shut down after ~1000 runs. This is believed to be due to RASPA printing random simulation info to logfiles, which bulked up quickly. 38db332 fixed this by removing relevant stderr printing on streaming.

Currently, libraspa shuts down after ~5000 runs. I think this is because of the remaining 7 MB of memory leak. 7 MB * 5000 = 35 GB, and my computer has 32 GB memory.

For context, the valgrind output as of today from:

▶ valgrind --log-file="valgrind.txt" --leak-check=full --show-leak-kinds=all ~/Dropbox/Github/RASPA2/simulations/bin/./simulate -i simulation.input

is 14,378 lines long and ends in

==3574== 
==3574== LEAK SUMMARY:
==3574==    definitely lost: 4,530 bytes in 9 blocks
==3574==    indirectly lost: 0 bytes in 0 blocks
==3574==      possibly lost: 0 bytes in 0 blocks
==3574==    still reachable: 7,569,987 bytes in 3,932 blocks
==3574==         suppressed: 0 bytes in 0 blocks
==3574== 

To fix, I'll have to go through this list.

Issue by patrickfuller
Tuesday Jul 30, 2013 at 19:31 GMT
Originally opened as https://github.com/numat/RASPA/issues/6

Segfaults are bad. Stop that.

Issue by patrickfuller
Friday Jul 26, 2013 at 20:54 GMT
Originally opened as https://github.com/numat/RASPA/issues/4

Right now, RASPA inputs (and optionally outputs) data as chemical files. This logic should be outsourced to a program like Open Babel. RASPA should then operate solely on a single JSON representation that open babel inputs and outputs, or the open babel OBMol object itself.

Hi,

I did the pip install with python 3.5 and copied the examples dir the Github files to my installation folder, however, I seem to have problems running some of the examples on my mac. For instance, I can run the MC_Methane_in_Box, MD_methane_in_Box_MSD examples it seems, but when I try to run RDF_of_Water_in_Box_MC or the Adsorption_of_Methane_in_MFI example, raspa2 seems to stall at the first calc step, giving output shown at the end of this message.

This is my computer step below. Any clues to what's wrong? How can I troubleshoot?

Output file

Compiler and run-time data
===========================================================================
RASPA 2.0
Compiled as a 64-bits application
Compiler: gcc 4.2.1 Compatible Apple LLVM 7.0.2 (clang-700.1.81)
Compile Date = Oct  7 2016, Compile Time = 01:30:09

Fri Oct  7 08:41:28 2016
Simulation started on Friday, October 07.
The start time was 08:41 AM.

Cpu data:    x86_64
Cpu Model:   MacBookPro12,1
Host name:   client224-21.wireless.umu.se
OS release:  14.5.0
OS type:     Darwin
OS version:  14F1912

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Starting simulation
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

[Init] Current cycle: 0 out of 10000
========================================================================================================

Net charge: 0 (F: 0, A: 0, C: 0)
Current Box:  24.83000   0.00000   0.00000 [A]
               0.00000  24.83000   0.00000 [A]
               0.00000   0.00000  24.83000 [A]
Box-lengths:  24.83000  24.83000  24.83000 Box-angles:   90.00000  90.00000  90.00000 [degrees]
Volume: 15308.41259 [A^3]

Amount of molecules per component:
----------------------------------------------------------------------------------------------------------------------------------------------------
Component 0 (Tip5p), current number of integer/fractional/reaction molecules: 512/0/0, density: 999.74825 [kg/m^3]
----------------------------------------------------------------------------------------------------------------------------------------------------
Degrees of freedom: 3072 0 3072 0
Number of Framework-atoms:      0
Number of Adsorbates:         512 (512 integer, 0 fractional, 0 reaction)
Number of Cations:              0 (0 integer, 0 fractional, reaction

Current total potential energy:           2973609.1799677564 [K]
    Current Host-Host energy:                     0.0000000000 [K]
    Current Host-Adsorbate energy:                0.0000000000 [K]
    Current Host-Cation energy:                   0.0000000000 [K]
    Current Adsorbate-Adsorbate energy:     2973609.1799677564 [K]
    Current Cation-Cation energy:                 0.0000000000 [K]
    Current Adsorbate-Cation energy:              0.0000000000 [K]