leetmaa / kmclib

A kinetic Monte Carlo Python/C++ library.

KMCLib - a general framework for lattice kinetic Monte Carlo (KMC) simulations

License and copying

Developed by Mikael Leetmaa at the Royal Institute of Technology (KTH), Sweden.
Copyright (c)  2012-2016  Mikael Leetmaa
Released under the GPLv3 license, see 'LICENSE.txt' for details.

When you use KMCLib in your research please cite the paper describing the code:

Mikael Leetmaa and Natalia V. Skorodumova
“KMCLib: A general framework for lattice kinetic Monte Carlo (KMC) simulations”
Comput. Phys. Commun. 185 (2014) 2340
DOI: 10.1016/j.cpc.2014.04.017

If you use version 1.1 or later I would also ask you to include this reference:

Mikael Leetmaa and Natalia V. Skorodumova
“KMCLib 1.1: Extended random number support and technical updates to the KMCLib general framework for kinetic Monte-Carlo simulations“
Comput. Phys. Commun.
DOI: 10.1016/j.cpc.2015.06.016

The mean square displacement algorithm is described here:

Mikael Leetmaa and Natalia V. Skorodumova
“Mean square displacements with error estimates from non-equidistant time-step kinetic Monte Carlo simulations“
Comput. Phys. Commun.
DOI: 10.1016/j.cpc.2015.02.006

KMCLib is now in version 2.0 alpha

KMCLib is a general framework for lattice kinetic Monte Carlo (KMC) simulations, to simulate the time evolution of systems of up to millions of particles in one, two or three dimensions. KMCLib is organized as a collection of Python frontend functions, classes and interfaces for performing efficient lattice KMC simulations, with all computationally heavy backend functionality implemented in C++.

Version 2.0 introduces support for having more than one particle per lattice site in the simulations. This was implemented to enable simulations of gas through porous solids as described in this paper:

Amber Mace, Mikael Leetmaa and Aatto Laaksonen
“Temporal Coarse Graining of CO2 and N2 Diffusion in Zeolite NaKA: From the Quantum Scale to the Macroscopic“
Journal of chemical theory and computation 11 (10), 4850-4860

Version 2.0 also comes with improved performance. A framework for writing custom rate calculators in C++ has been added for performance sensitive applications. Once your custom rate calculator is prototyped and tested in Python you can port it to C++ for increased performance. A caching mechanism for custom rates is now also in place, that can significantly reduce computational time for time consuming custom rates calculations.

The combination of features makes KMCLib unique

• Python user interface - well documented, easily extended.
• C++ backend library for maximizing efficiency.
• Easy to prototype KMC models - no need to recompile source to run new models.
• Arbitrarily complex elementary processes can be used.
• On-the-fly evaluation of custom rate expressions written in Python.
• Built in on-the-fly mean square displacement (MSD) analysis to facilitate diffusion studies.
• MPI parallelism without loss of accuracy.

Well documented with usage examples and install instructions

The code manual (http://leetmaa.github.io/KMCLib/manual-v1.1/) includes full documentation of the Python interface and several usage examples, as well as installation instructions for both Linux and Mac.

There is at the time of writing no manual for version 2.0. All features in version 1.1 should be unchanged however. If ever in doubt please check the source code for details.

Known issues

Version 2.0 is still in an alpha stage. The set of features might change before the full version 2.0, and bugs may be found and fixed, however the quality of the code at this stage should meet the same standards with respect to quality as the previous full version 1.1. There are at the time of writing no known major bugs or issues, but as always, if you happen to find any bugs or issues, or if you have suggestions for improvements, please let me know.

Obtain a copy

The program is distributed under the GPLv3 license and can be obtained from the KMCLib git repository https://github.com/leetmaa/KMCLib/releases/tag/v2.0-a1

Use KMCLib in your own research

If you would be interested to use this code in your research and need any assistance, or if you are interested in collaborations, please don't hesitate to send me an e-mail: [email protected]

Mikael Leetmaa, Mars 28 2016

kmclib's Issues

Question about cutoff in CustomRateCalculator

I am trying to apply KMCLib on diffusion problem within a hexagonal lattice.
I want the diffusion rate to be calculated from nearest neighbor atoms so I tried CustomRateCalculator.
As there seems to be no explicit nearest neighbor list so I thought that defining cutoff might work.
However the cutoff is seems to be like:

The distance D between a site and the center is calculated as
D = sqrt(x^2 + y^2 + z^2)
where (x,y,z) is the internal coordinate of the site.
Only the sites with D < cutoff will be counted.

So cutoff only works when the lattice is a cubic with a = b = c.
Since I have a hexagonal lattice, in which, for example, the distance between (0,0,0) and (1,1,0) is just the same as that between (0,0,0) and (1,0,0), while setting cutoff to 1 just includes (1,0,0) but excludes (1,1,0).
Is there any way to define cutoff as an absolute distance?

Installation error in cluster

Hi, I succeeded in installing it on my own redhat. But when installing on cluster which have a lot c++, mpi modules, it failed. I doubt the reason comes from cmake. The make file used the /user/bin/c++ instead of provided gcc path. Could you fix this error or tell me how to fix it?

Best,
Albert

Abort Trap 6 mistake

Dear KMCLib developer,
Thank you for this amazing software. I've been searching for similar programs for a long time.
The installation is successful, but when I do "python utest.py", an error occured:

Fatal Python error: PyThreadState_Get: no current thread
Abort trap: 6

Could you help me fix this ?
Thanks,
Zhengda

Typo in MSD output

The header of the output produced by printResults has a key 'DSD_y' rather than 'MSD_y'.

KMCLib/python/src/KMCLib/Analysis/OnTheFlyMSD.py

Line 289 in 4513acc

stream.write("%11s %11s %11s %11s %11s %11s %11s %11s %11s %11s %11s %11s %11s %11s %11s %11s\n"%("TIME ", "MSD_x ", "DSD_y ", "MSD_z ", "MSD_xy ", "MSD_xz ", "MSD_yz ", "MSD_xyz ", "STD_x ", "STD_y ", "STD_z ", "STD_xy ", "STD_xz ", "STD_yz ", "STD_xyz ", "N_eff"))

neighbour list in custom rate calculator

Does CustomRateCalculator class has neighbour list of the central coordinate available through backend?

1. In KMCLib/python/functest/IsingSpin/IsingSpinTest.py the rate function requires neighbours of the central coordinate at which a flip of spin is made. I've checked all the associated files and this information is not explicitly specified when calling the CustomRateCalculator. However, as per the calculations in the rate function, the elements_before and elements_after arrays should have the neighbours at indices 1-4.

2. Additionally, if the custom rate is for a diffusive hop on orthogonal lattice, e.g., in KMCLib/python/functest/OnTheFlyRateCalculator/OnTheFlyRateCalculatorTest.py, how the indices are defined for next nearest neghbours. Pasting the relevant portion from code below:

   Before move the central particle has neighbour indices 1, 2, 3, 4.

    # After the move the central particle has meighbour indices,
    # if we move to the right, 0, 7, 8, 12
    # if we move up,           0, 6, 8, 11
    # if we move down,         0, 5, 7, 10
    # if we move left,         0, 5, 6, 9
   

MacOS 10.12.1 build

Hi, I'm trying to build for MacOS using homebrew to install swig. I get through the unit tests, but make install fails because a bunch of python symbols are not found:

[ 83%] Linking CXX shared module _Custom.so
cd /Users/scott/Documents/Code/git/KMCLib/c++/build/wrap && /usr/local/Cellar/cmake/3.6.2/bin/cmake -E cmake_link_script CMakeFiles/_Custom.dir/link.txt --verbose=1
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang++   -O3 -fPIC -Wall -Wextra -Werror -pedantic -stdlib=libc++  -std=c++11 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk -bundle -Wl,-headerpad_max_install_names  -o _Custom.so CMakeFiles/_Custom.dir/customPYTHON_wrap.cxx.o -framework python ../custom/libcustom.a ../src/libsrc.a 
Undefined symbols for architecture x86_64:
  "_PyInstanceMethod_New", referenced from:
      SWIG_PyInstanceMethod_New(_object*, _object*) in customPYTHON_wrap.cxx.o
  "_PyModule_Create2", referenced from:
      _PyInit__Custom in customPYTHON_wrap.cxx.o
  "_PyUnicode_Concat", referenced from:
      SwigPyObject_repr(SwigPyObject*) in customPYTHON_wrap.cxx.o
  "_PyUnicode_DecodeUTF8", referenced from:
      SWIG_From_std_string(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in customPYTHON_wrap.cxx.o
  "_PyUnicode_FromFormat", referenced from:
      SwigPyObject_repr(SwigPyObject*) in customPYTHON_wrap.cxx.o
      SwigPyPacked_repr(SwigPyPacked*) in customPYTHON_wrap.cxx.o
      SwigPyPacked_str(SwigPyPacked*) in customPYTHON_wrap.cxx.o
  "_PyUnicode_FromString", referenced from:
      SWIG_Python_GetSwigThis(_object*) in customPYTHON_wrap.cxx.o
      SWIG_Python_NewPointerObj(_object*, void*, swig_type_info*, int) in customPYTHON_wrap.cxx.o
      SWIG_Python_DestroyModule(_object*) in customPYTHON_wrap.cxx.o
      SwigPyPacked_str(SwigPyPacked*) in customPYTHON_wrap.cxx.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [wrap/_Custom.so] Error 1
make[1]: *** [wrap/CMakeFiles/_Custom.dir/all] Error 2
make: *** [all] Error 2

I installed swig using homebrew and not macports, and I wonder if something is missing?

[Compilation on macOS] Unidentified CXX compiler version

I would like to report some testings on macOS. Following the installation guides to install KMCLib via clang + MPI on macOS 10.15 throws unsupported compiler error.

Steps to reproduce

• System: macOS 10.15, AppleClang 11.0 (Clang 3.9)
• MPI version: open-mpi 4.0.3 based on clang-3.9 (distributed via Homebrew)
  -Running command under the c++/build directory:

CC=clang CXX="clang++ -stdlib=libc++" cmake -DMPI=mpicxx ..

• Error message:

CMake Error at CMakeLists.txt:103 (message):
  Invalid CXX compiler.  Only g++, Intel and Clang supported

Possible causes

The newest version of open-mpi based on clang is recognized as System CXX compiler with MPI wrapping by CMake, which makes the rules in CMakeLists invalid.

Possible solutions

Update CMakeLists.txt so that when user puts CXX=mpicxx it can automatically recognise the MPI option.

Compilation Error for make test.x on Ubuntu 18.04

Hi,
I have tried to compile the module on Ubuntu 18.04, using gcc, g++ and mpicxx. All seems to be fine, until I try to run the test.

Indeed, by typing make test.x in the c++/build directory, I get the following error:

/home/xelad/KMCLib-2.0-a1/c++/unittest/test_interactions.cpp:146:25: error: the compiler can assume that the address of 'rc' will never be NULL [-Werror=address] CPPUNIT_ASSERT( &rc != NULL ); ^ /home/xelad/KMCLib-2.0-a1/c++/externals/include/cppunit/TestAssert.h:131:37: note: in definition of macro 'CPPUNIT_ASSERT' ( CPPUNIT_NS::Asserter::failIf( !(condition), \ ^~~~~~~~~ cc1plus: all warnings being treated as errors unittest/CMakeFiles/unittest.dir/build.make:185: recipe for target 'unittest/CMakeFiles/unittest.dir/test_interactions.cpp.o' failed make[3]: *** [unittest/CMakeFiles/unittest.dir/test_interactions.cpp.o] Error 1 make[3]: Leaving directory '/home/xelad/KMCLib-2.0-a1/c++/build' CMakeFiles/Makefile2:233: recipe for target 'unittest/CMakeFiles/unittest.dir/all' failed make[2]: *** [unittest/CMakeFiles/unittest.dir/all] Error 2 make[2]: Leaving directory '/home/xelad/KMCLib-2.0-a1/c++/build' CMakeFiles/Makefile2:208: recipe for target 'unittest/CMakeFiles/test.x.dir/rule' failed make[1]: *** [unittest/CMakeFiles/test.x.dir/rule] Error 2 make[1]: Leaving directory '/home/xelad/KMCLib-2.0-a1/c++/build' Makefile:193: recipe for target 'test.x' failed make: *** [test.x] Error 2

I have read the known issue and I have found that you suggested to comment the line "CPPUNIT_ASSERT( &rc != NULL );"

However, by doing that, I got another error:

/home/xelad/KMCLib-2.0-a1/c++/unittest/test_interactions.cpp:145:28: error: unused variable 'rc' [-Werror=unused-variable] const RateCalculator & rc = interactions.rateCalculator(); ^~ cc1plus: all warnings being treated as errors unittest/CMakeFiles/unittest.dir/build.make:185: recipe for target 'unittest/CMakeFiles/unittest.dir/test_interactions.cpp.o' failed make[3]: *** [unittest/CMakeFiles/unittest.dir/test_interactions.cpp.o] Error 1 make[3]: Leaving directory '/home/xelad/KMCLib-2.0-a1/c++/build' CMakeFiles/Makefile2:233: recipe for target 'unittest/CMakeFiles/unittest.dir/all' failed make[2]: *** [unittest/CMakeFiles/unittest.dir/all] Error 2 make[2]: Leaving directory '/home/xelad/KMCLib-2.0-a1/c++/build' CMakeFiles/Makefile2:208: recipe for target 'unittest/CMakeFiles/test.x.dir/rule' failed make[1]: *** [unittest/CMakeFiles/test.x.dir/rule] Error 2 make[1]: Leaving directory '/home/xelad/KMCLib-2.0-a1/c++/build' Makefile:193: recipe for target 'test.x' failed make: *** [test.x] Error 2

Can you please suggest me how to solve this?

There were some problems running the test file?

when I running the Diffusion1DTest.py test file and KMC operation terminated suddenly

Then the error is reported as follows：
Diffusion1DTest.txt

ERROR: testRun (main.Diffusion1DTest)
Run the model and check the results.

Traceback (most recent call last):
File "Diffusion1DTest.py", line 119, in testRun
fit = numpy.linalg.lstsq(A, b, rcond=None)
File "/usr/lib64/python2.7/site-packages/numpy/linalg/linalg.py", line 1838, in lstsq
0, work, -1, iwork, 0)
TypeError: a float is required

---

Ran 1 test in 13.851s

FAILED (errors=1)

Does anyone know what the problem is？

linking libstdc++ statically

Hi Leetmaa:
Is it better to link libstdc++ statically by adding -static-libstdc++ compiler option for compatible working in different linux?

ShaoZhengjiang

python-dev / Python.h

Hello,

Just a quick comment regarding installation on ubuntu 18.04.
For the final make (make test.x worked fine) Python.h wasn't found.

Solution:
sudo apt install python-dev
locate Python.h # find where it is
in CMakeLists.txt:
include_directories(where_it_is)

Thanks for making this available

There were some problems running the utest.py test file?

when I running the utest.py test file and KMC operation terminated suddenly

Then the error is reported as follows：

Traceback (most recent call last):
File "utest.py", line 13, in
from KMCLibTest import KMCLibTests
File "/home/biao/KMCLib-master/python/unittest/KMCLibTest/KMCLibTests.py", line 14, in
from .CoreComponents import CoreComponentsTests
File "/home/biao/KMCLib-master/python/unittest/KMCLibTest/CoreComponents/CoreComponentsTests.py", line 15, in
from .KMCLatticeModelTest import KMCLatticeModelTest
File "/home/biao/KMCLib-master/python/unittest/KMCLibTest/CoreComponents/KMCLatticeModelTest.py", line 604
exec(compile(open(trajectory_filename, "rb").read(), trajectory_filename, 'exec'), global_dict, local_dict)
SyntaxError: unqualified exec is not allowed in function 'testRunNoMatch' it contains a nested function with free variables

Does anyone know what the problem is？

code for monomer jump on hexagonal lattice?

Please tell me how to write a code for monomer jump on hexagonal lattice.
Thank you.

AssertionError

Hello
While I was running the 'utest.py' file, the final result was shown as

======================================================================
FAIL: testScript (KMCLibTest.CoreComponents.KMCConfigurationTest.KMCConfigurationTest)
Test that we can generate a valid script.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/zyzhang/KMCLib/python/unittest/KMCLibTest/CoreComponents/KMCConfigurationTest.py", line 678, in testScript
    self.assertEqual(script, ref_script)
AssertionError: "\n# -----------------------------------------------------------------------------\n# Unit cell\n\ncell_vectors = [[   2.800000e+00,   0.000000e+00,   0.000000e+00],\n                [   0.000000e+00,   3.200000e+00,   0.000000e+00],\n                [   0.000000e+00,   5.000000e-01,   3.000000e+00]]\n\nbasis_points = [[   0.000000e+00,   0.000000e+00,   0.000000e+00]]\n\nunit_cell = KMCUnitCell(\n    cell_vectors=cell_vectors,\n    basis_points=basis_points)\n\n# -----------------------------------------------------------------------------\n# Lattice\n\nlattice = KMCLattice(\n    unit_cell=unit_cell,\n    repetitions=(1,1,1),\n    periodic=(False, False, False))\n\n# -----------------------------------------------------------------------------\n# Configuration\n\ntypes = ['ThisIsTheTypeOfMyOnlySiteInThisUnrealisticallyShortStructure']\n\npossible_types = ['A','CDEFGHI','ThisIsTheTypeOfMyOnlySiteInThisUnrealisticallyShortStructure',\n                  'B']\n\nconfig = KMCConfiguration(\n    lattice=lattice,\n    types=types,\n    possible_types=possible_types)\n" != "\n# -----------------------------------------------------------------------------\n# Unit cell\n\ncell_vectors = [[   2.800000e+00,   0.000000e+00,   0.000000e+00],\n                [   0.000000e+00,   3.200000e+00,   0.000000e+00],\n                [   0.000000e+00,   5.000000e-01,   3.000000e+00]]\n\nbasis_points = [[   0.000000e+00,   0.000000e+00,   0.000000e+00]]\n\nunit_cell = KMCUnitCell(\n    cell_vectors=cell_vectors,\n    basis_points=basis_points)\n\n# -----------------------------------------------------------------------------\n# Lattice\n\nlattice = KMCLattice(\n    unit_cell=unit_cell,\n    repetitions=(1,1,1),\n    periodic=(False, False, False))\n\n# -----------------------------------------------------------------------------\n# Configuration\n\ntypes = ['ThisIsTheTypeOfMyOnlySiteInThisUnrealisticallyShortStructure']\n\npossible_types = ['ThisIsTheTypeOfMyOnlySiteInThisUnrealisticallyShortStructure',\n                  'A','B','CDEFGHI']\n\nconfig = KMCConfiguration(\n    lattice=lattice,\n    types=types,\n    possible_types=possible_types)\n"

======================================================================
FAIL: testRunInitialMatch (KMCLibTest.CoreComponents.KMCLatticeModelTest.KMCLatticeModelTest)
Test the output of initial matchinformation from a run of the A-B flip model.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/zyzhang/KMCLib/python/unittest/KMCLibTest/CoreComponents/KMCLatticeModelTest.py", line 493, in testRunInitialMatch
    self.assertTrue(ref in stream_1.getvalue())
AssertionError: False is not true

----------------------------------------------------------------------
Ran 190 tests in 1.675s

FAILED (failures=2)

How can such an error solved?

python test fail

I am compiling with CentOS, gcc/7.3.0, and python 2.7.18. there are some errors. Is there specific requirements for python version?

raceback (most recent call last):
File "/home/wenjiang0716/KMC_gcc_7.3.0/KMCLib/python/unittest/KMCLibTest/Analysis/OnTheFlyMSDTest.py", line 568, in testPrintResults
msd.printResults(stream)
File "/home/wenjiang0716/KMC_gcc_7.3.0/KMCLib/python/src/KMCLib/Analysis/OnTheFlyMSD.py", line 288, in printResults
stream.write("%11s %11s %11s %11s %11s %11s %11s %11s %11s %11s %11s %11s %11s %11s %11s %11s\n"%("TIME ", "MSD_x ", "MSD_y ", "MSD_z ", "MSD_xy ", "MSD_xz ", "MSD_yz ", "MSD_xyz ", "STD_x ", "STD_y ", "STD_z ", "STD_xy ", "STD_xz ", "STD_yz ", "STD_xyz ", "N_eff"))
TypeError: unicode argument expected, got 'str'

======================================================================
ERROR: testPrintResults (KMCLibTest.Analysis.TimeStepDistributionTest.TimeStepDistributionTest)
Test the time step distribution print result function.

Traceback (most recent call last):
File "/home/wenjiang0716/KMC_gcc_7.3.0/KMCLib/python/unittest/KMCLibTest/Analysis/TimeStepDistributionTest.py", line 139, in testPrintResults
tsd.printResults(stream)
File "/home/wenjiang0716/KMC_gcc_7.3.0/KMCLib/python/src/KMCLib/Analysis/TimeStepDistribution.py", line 108, in printResults
stream.write("%10.5f %10i %20.15f\n"%(t, v, n))
TypeError: unicode argument expected, got 'str'

======================================================================
ERROR: testPrintResults (KMCLibTest.Analysis.ProcessStatisticsTest.ProcessStatisticsTest)
Test that we can print the results

Traceback (most recent call last):
File "/home/wenjiang0716/KMC_gcc_7.3.0/KMCLib/python/unittest/KMCLibTest/Analysis/ProcessStatisticsTest.py", line 188, in testPrintResults
ps.printResults(stream)
File "/home/wenjiang0716/KMC_gcc_7.3.0/KMCLib/python/src/KMCLib/Analysis/ProcessStatistics.py", line 102, in printResults
stream.write("%15s %15s %15s %12s\n"%(" time (t)", " count (n)", "(dn/dt) ", "(n/t)"))
TypeError: unicode argument expected, got 'str'

======================================================================
ERROR: testPrintResults (KMCLibTest.Analysis.CompositionTest.CompositionTest)
Test that we can print the results

Traceback (most recent call last):
File "/home/wenjiang0716/KMC_gcc_7.3.0/KMCLib/python/unittest/KMCLibTest/Analysis/CompositionTest.py", line 215, in testPrintResults
cc.printResults(stream)
File "/home/wenjiang0716/KMC_gcc_7.3.0/KMCLib/python/src/KMCLib/Analysis/Composition.py", line 97, in printResults
stream.write(format_str_1%tuple(types_str))
TypeError: unicode argument expected, got 'str'

======================================================================
ERROR: testRunInitialMatch (KMCLibTest.CoreComponents.KMCLatticeModelTest.KMCLatticeModelTest)
Test the output of initial matchinformation from a run of the A-B flip model.

Traceback (most recent call last):
File "/home/wenjiang0716/KMC_gcc_7.3.0/KMCLib/python/unittest/KMCLibTest/CoreComponents/KMCLatticeModelTest.py", line 482, in testRunInitialMatch
ab_flip_model.run(control_parameters=control_parameters)
File "/home/wenjiang0716/KMC_gcc_7.3.0/KMCLib/python/src/KMCLib/CoreComponents/KMCLatticeModel.py", line 125, in run
prettyPrint(msg)
File "/home/wenjiang0716/KMC_gcc_7.3.0/KMCLib/python/src/KMCLib/Utilities/PrintUtilities.py", line 31, in prettyPrint
output.write(msg)
TypeError: unicode argument expected, got 'str'

======================================================================
ERROR: testPrettyPrint (KMCLibTest.Utilities.PrintUtilitiesTest.PrintUtilitiesTest)
Test that we can call the pretty print function.

Traceback (most recent call last):
File "/home/wenjiang0716/KMC_gcc_7.3.0/KMCLib/python/unittest/KMCLibTest/Utilities/PrintUtilitiesTest.py", line 35, in testPrettyPrint
prettyPrint(ref_str)
File "/home/wenjiang0716/KMC_gcc_7.3.0/KMCLib/python/src/KMCLib/Utilities/PrintUtilities.py", line 31, in prettyPrint
output.write(msg)
TypeError: unicode argument expected, got 'str'

======================================================================
ERROR: testPrintHeader (KMCLibTest.Utilities.PrintUtilitiesTest.PrintUtilitiesTest)
Test the print header function.

Traceback (most recent call last):
File "/home/wenjiang0716/KMC_gcc_7.3.0/KMCLib/python/unittest/KMCLibTest/Utilities/PrintUtilitiesTest.py", line 71, in testPrintHeader
printHeader()
File "/home/wenjiang0716/KMC_gcc_7.3.0/KMCLib/python/src/KMCLib/Utilities/PrintUtilities.py", line 46, in printHeader
prettyPrint("# -----------------------------------------------------------------------------", output)
File "/home/wenjiang0716/KMC_gcc_7.3.0/KMCLib/python/src/KMCLib/Utilities/PrintUtilities.py", line 31, in prettyPrint
output.write(msg)
TypeError: unicode argument expected, got 'str'

======================================================================
FAIL: testScript (KMCLibTest.CoreComponents.KMCConfigurationTest.KMCConfigurationTest)
Test that we can generate a valid script.

Traceback (most recent call last):
File "/home/wenjiang0716/KMC_gcc_7.3.0/KMCLib/python/unittest/KMCLibTest/CoreComponents/KMCConfigurationTest.py", line 676, in testScript
self.assertEqual(script, ref_script)
AssertionError: "\n# -----------------------------------------------------------------------------\n# Unit cell\n\ncell_vectors = [[ 2.800000e+00, 0.000000e+00, 0.000000e+00],\n [ 0.000000e+00, 3.200000e+00, 0.000000e+00],\n [ 0.000000e+00, 5.000000e-01, 3.000000e+00]]\n\nbasis_points = [[ 0.000000e+00, 0.000000e+00, 0.000000e+00]]\n\nunit_cell = KMCUnitCell(\n cell_vectors=cell_vectors,\n basis_points=basis_points)\n\n# -----------------------------------------------------------------------------\n# Lattice\n\nlattice = KMCLattice(\n unit_cell=unit_cell,\n repetitions=(1,1,1),\n periodic=(False, False, False))\n\n# -----------------------------------------------------------------------------\n# Configuration\n\ntypes = ['ThisIsTheTypeOfMyOnlySiteInThisUnrealisticallyShortStructure']\n\npossible_types = ['A','CDEFGHI','ThisIsTheTypeOfMyOnlySiteInThisUnrealisticallyShortStructure',\n 'B']\n\nconfig = KMCConfiguration(\n lattice=lattice,\n types=types,\n possible_types=possible_types)\n" != "\n# -----------------------------------------------------------------------------\n# Unit cell\n\ncell_vectors = [[ 2.800000e+00, 0.000000e+00, 0.000000e+00],\n [ 0.000000e+00, 3.200000e+00, 0.000000e+00],\n [ 0.000000e+00, 5.000000e-01, 3.000000e+00]]\n\nbasis_points = [[ 0.000000e+00, 0.000000e+00, 0.000000e+00]]\n\nunit_cell = KMCUnitCell(\n cell_vectors=cell_vectors,\n basis_points=basis_points)\n\n# -----------------------------------------------------------------------------\n# Lattice\n\nlattice = KMCLattice(\n unit_cell=unit_cell,\n repetitions=(1,1,1),\n periodic=(False, False, False))\n\n# -----------------------------------------------------------------------------\n# Configuration\n\ntypes = ['ThisIsTheTypeOfMyOnlySiteInThisUnrealisticallyShortStructure']\n\npossible_types = ['ThisIsTheTypeOfMyOnlySiteInThisUnrealisticallyShortStructure',\n 'A','B','CDEFGHI']\n\nconfig = KMCConfiguration(\n lattice=lattice,\n types=types,\n possible_types=possible_types)\n"

---

Ran 190 tests in 5.015s

FAILED (failures=1, errors=7)

KMCRateCalculatorPlugin question

Hi, Mikael, I find I can't input any parameters for my own rate calculator. In KMCInteractions, the rate_calculator under setRateCalculator should be a class, not object. I can't provide any specific parameters into my own rate calculator. For example, I want to make the rate to be temperature related. I can't input the temperature except use a global variable. Do I understand correct?

Best,
Albert

wrong command in the content in KMCLib 1.1 documentation - Make system

in the paragraph Make system:

Make system
The make system is based on CMake. Installing CMake can be done by typing on Ubuntu:

sudo apt-get install swig

and on Mac OSX using macports:

sudo port install swig && sudo port install swig-python

The command for installation of CMake is wrong, it is the installation of swig which is the same with the next paragraph.

I am using ubuntu 14, is Cmake 3.5.1 proper for kMClib?

I am installing KMCLib-2.0-a1 in ubuntu 15.04. I followed the installation steps. I am getting an error message when I do 'make test.x' in build directory. Can you please solve this problem.

I am installing KMCLib-2.0-a1 in ubuntu 15.04. I followed the installation steps. I am getting an error message when I do 'make test.x' in the build directory. Can you please solve this problem.
Thanks in Advance.

home/rao/Downloads/KMCLib-2.0-a1/c++/unittest/test_hash.cpp:177:40: error: large integer implicitly truncated to unsigned type [-Werror=overflow]
const unsigned long int ref0 = 17780468236463825071u;
^
cc1plus: all warnings being treated as errors
unittest/CMakeFiles/unittest.dir/build.make:80: recipe for target 'unittest/CMakeFiles/unittest.dir/test_hash.cpp.o' failed
make[3]: *** [unittest/CMakeFiles/unittest.dir/test_hash.cpp.o] Error 1
make[3]: Leaving directory '/home/rao/Downloads/KMCLib-2.0-a1/c++/build'
CMakeFiles/Makefile2:212: recipe for target 'unittest/CMakeFiles/unittest.dir/all' failed
make[2]: *** [unittest/CMakeFiles/unittest.dir/all] Error 2
make[2]: Leaving directory '/home/rao/Downloads/KMCLib-2.0-a1/c++/build'
CMakeFiles/Makefile2:189: recipe for target 'unittest/CMakeFiles/test.x.dir/rule' failed
make[1]: *** [unittest/CMakeFiles/test.x.dir/rule] Error 2
make[1]: Leaving directory '/home/rao/Downloads/KMCLib-2.0-a1/c++/build'
Makefile:180: recipe for target 'test.x' failed
make: *** [test.x] Error 2

Problem in running utest.py: ModuleNotFoundError: No module named 'Analysis'

I use python 3.8 for installing KMCLib version 2.0-a1

I have an error, it says no module named 'Analysis':
Traceback (most recent call last): File "utest.py", line 13, in <module> from KMCLibTest import KMCLibTests File "/home/azka/02_Software/KMCLib-2.0-a1/python/unittest/KMCLibTest/KMCLibTests.py", line 12, in <module> from Analysis import AnalysisTests ModuleNotFoundError: No module named 'Analysis'

Eventhough I had installed it before successfully
$ python3.8 -m pip install analysis Requirement already satisfied: analysis in /home/azka/anaconda3/envs/kmclib2/lib/python3.8/site-packages (0.1.7)

Do you know why does this happen?

Count KMCProcess events

I've read through the documentation and I can't figure out how to count the number of times an event fires without printing the trajectory information or launching an analysis plugin after every step. Is there a way to print/record a running tally of how many times an event type has been fired?