{"action":"opened","issue":{"url":"https://api.github.com/repos/mhoffman/kmos/issues/45","repository_url":"https://api.github.com/repos/mhoffman/kmos","labels_url":"https://api.github.com/repos/mhoffman/kmos/issues/45/labels{/name}","comments_url":"https://api.github.com/repos/mhoffman/kmos/issues/45/comments","events_url":"https://api.github.com/repos/mhoffman/kmos/issues/45/events","html_url":"https://github.com/mhoffman/kmos/issues/45","id":143800744,"number":45,"title":"no reasult like expected---firstmodel","user":{"login":"jiangwangzhagn","id":18079695,"avatar_url":"https://avatars.githubusercontent.com/u/18079695?v=3","gravatar_id":"","url":"https://api.github.com/users/jiangwangzhagn","html_url":"https://github.com/jiangwangzhagn","followers_url":"https://api.github.com/users/jiangwangzhagn/followers","following_url":"https://api.github.com/users/jiangwangzhagn/following{/other_user}","gists_url":"https://api.github.com/users/jiangwangzhagn/gists{/gist_id}","starred_url":"https://api.github.com/users/jiangwangzhagn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jiangwangzhagn/subscriptions","organizations_url":"https://api.github.com/users/jiangwangzhagn/orgs","repos_url":"https://api.github.com/users/jiangwangzhagn/repos","events_url":"https://api.github.com/users/jiangwangzhagn/events{/privacy}","received_events_url":"https://api.github.com/users/jiangwangzhagn/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2016-03-27T11:35:52Z","updated_at":"2016-03-27T11:35:52Z","closed_at":null,"body":"following the instructions, everything seems OK. And I wait for the result, but after over10 hours, the kmos is still running!!\r\n\r\n![screenshot from 2016-03-27 07-29-05](https://cloud.githubusercontent.com/assets/18079695/14065193/6870b980-f3ee-11e5-9ab6-d35895df8c6f.png)\r\n\r\n`In [1]: from kmos.types import *\r\n\r\nIn [2]: from kmos.io import *\r\n\r\nIn [3]: import numpy as np\r\n\r\nIn [4]: os.getcwd()\r\nOut[4]: '/home/jiangzhen'\r\n\r\nIn [5]: pt = Project()\r\n\r\nIn [6]: pt.set_meta(author = 'Your Name',\r\n   ...:             email = 'your.name@server.com',\r\n   ...:             model_name = 'MyFirstModel',\r\n   ...:             model_dimension = 2,)\r\n\r\nIn [7]: pt.add_species(name='empty')\r\nOut[7]: [SPECIES] Name: empty Color: no color set.\r\n\r\nIn [8]: pt.add_species(name='CO',\r\n   ...:                representation=\"Atoms('CO',[[0,0,0],[0,0,1.2]])\")\r\nOut[8]: [SPECIES] Name: CO Color: no color set.\r\n\r\nIn [9]: layer = pt.add_layer(name='simple_cubic')\r\n\r\nIn [10]: layer.sites.append(Site(name='hollow', pos='0.5 0.5 0.5',\r\n   ....:                         default_species='empty'))\r\n\r\nIn [11]: pt.lattice.cell = np.diag([3.5, 3.5, 10])\r\n\r\nIn [12]: pt.add_parameter(name='T', value=600., adjustable=True, min=400, max=800)\r\nOut[12]: [PARAMETER] Name: T Value: 600.0\r\n\r\nIn [13]: pt.add_parameter(name='p_CO', value=1., adjustable=True, min=1e-10, max=1.e2)\r\nOut[13]: [PARAMETER] Name: p_CO Value: 1.0\r\n\r\nIn [14]: pt.add_parameter(name='A', value='(3.5*angstrom)**2')\r\nOut[14]: [PARAMETER] Name: A Value: (3.5*angstrom)**2\r\n\r\nIn [15]: pt.add_parameter(name='deltaG', value='-0.5', adjustable=True,\r\n   ....:                            min=-1.3, max=0.3)\r\nOut[15]: [PARAMETER] Name: deltaG Value: -0.5\r\n\r\nIn [16]: coord = pt.lattice.generate_coord('hollow.(0,0,0).simple_cubic')\r\n\r\nIn [17]: pt.add_process(name='CO_adsorption',\r\n   ....:                conditions=[Condition(coord=coord, species='empty')],\r\n   ....:                actions=[Action(coord=coord, species='CO')],\r\n   ....:                rate_constant='p_CO*bar*A/sqrt(2*pi*umass*m_CO/beta)')\r\nOut[17]: \r\n[PROCESS] Name:CO_adsorption\r\n     Rate: p_CO*bar*A/sqrt(2*pi*umass*m_CO/beta)\r\nConditions: [[COND_ACT] Species: empty Coord:[COORD] hollow.(0, 0, 0).simple_cubic\r\n]\r\nActions: [[COND_ACT] Species: CO Coord:[COORD] hollow.(0, 0, 0).simple_cubic\r\n]\r\n\r\nIn [18]: pt.add_process(name='CO_desorption',\r\n   ....:                conditions=[Condition(coord=coord, species='CO')],\r\n   ....:                actions=[Action(coord=coord, species='empty')],\r\n   ....:                rate_constant='p_CO*bar*A/sqrt(2*pi*umass*m_CO/beta)*exp(beta*deltaG*eV)')\r\nOut[18]: \r\n[PROCESS] Name:CO_desorption\r\n     Rate: p_CO*bar*A/sqrt(2*pi*umass*m_CO/beta)*exp(beta*deltaG*eV)\r\nConditions: [[COND_ACT] Species: CO Coord:[COORD] hollow.(0, 0, 0).simple_cubic\r\n]\r\nActions: [[COND_ACT] Species: empty Coord:[COORD] hollow.(0, 0, 0).simple_cubic\r\n]\r\n\r\nIn [19]: pt.filename = 'myfirst_kmc.xml'\r\n\r\nIn [20]: pt.save()\r\n\r\nIn [21]: import kmos.cli\r\n\r\nIn [22]: kmos.cli.main('export myfirst_kmc.xml')\r\nNo export path provided. Exporting to myfirst_kmc_local_smart\r\n/usr/local/lib/python2.7/dist-packages/kmos\r\nUnknown vendor: \"gfortran\"\r\nrunning build\r\nrunning config_cc\r\nunifing config_cc, config, build_clib, build_ext, build commands --compiler options\r\nrunning config_fc\r\nunifing config_fc, config, build_clib, build_ext, build commands --fcompiler options\r\nrunning build_src\r\nbuild_src\r\nbuilding extension \"f2py_selected_kind\" sources\r\nf2py options: []\r\nf2py:> /tmp/tmpauT4p9/src.linux-x86_64-2.7/f2py_selected_kindmodule.c\r\ncreating /tmp/tmpauT4p9/src.linux-x86_64-2.7\r\nReading fortran codes...\r\n\tReading file 'f2py_selected_kind.f90' (format:free)\r\nPost-processing...\r\n\tBlock: f2py_selected_kind\r\n\t\t\tBlock: kind\r\n\t\t\t\tBlock: real_kind\r\n\t\t\t\tBlock: int_kind\r\nPost-processing (stage 2)...\r\n\tBlock: f2py_selected_kind\r\n\t\tBlock: unknown_interface\r\n\t\t\tBlock: kind\r\n\t\t\t\tBlock: real_kind\r\n\t\t\t\tBlock: int_kind\r\nBuilding modules...\r\n\tBuilding module \"f2py_selected_kind\"...\r\n\t\tConstructing F90 module support for \"kind\"...\r\n\t\t\tConstructing wrapper function \"kind.real_kind\"...\r\n\t\t\t  kind_value = real_kind([p,r])\r\n\t\t\tConstructing wrapper function \"kind.int_kind\"...\r\n\t\t\t  kind_value = int_kind([p,r])\r\n\tWrote C/API module \"f2py_selected_kind\" to file \"/tmp/tmpauT4p9/src.linux-x86_64-2.7/f2py_selected_kindmodule.c\"\r\n\tFortran 90 wrappers are saved to \"/tmp/tmpauT4p9/src.linux-x86_64-2.7/f2py_selected_kind-f2pywrappers2.f90\"\r\n  adding '/tmp/tmpauT4p9/src.linux-x86_64-2.7/fortranobject.c' to sources.\r\n  adding '/tmp/tmpauT4p9/src.linux-x86_64-2.7' to include_dirs.\r\ncopying /usr/lib/python2.7/dist-packages/numpy/f2py/src/fortranobject.c -> /tmp/tmpauT4p9/src.linux-x86_64-2.7\r\ncopying /usr/lib/python2.7/dist-packages/numpy/f2py/src/fortranobject.h -> /tmp/tmpauT4p9/src.linux-x86_64-2.7\r\n  adding '/tmp/tmpauT4p9/src.linux-x86_64-2.7/f2py_selected_kind-f2pywrappers2.f90' to sources.\r\nbuild_src: building npy-pkg config files\r\nrunning build_ext\r\ncustomize UnixCCompiler\r\ncustomize UnixCCompiler using build_ext\r\ncustomize Gnu95FCompiler\r\nFound executable /usr/bin/gfortran\r\ncustomize Gnu95FCompiler using build_ext\r\nbuilding 'f2py_selected_kind' extension\r\ncompiling C sources\r\nC compiler: x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC\r\n\r\ncreating /tmp/tmpauT4p9/tmp\r\ncreating /tmp/tmpauT4p9/tmp/tmpauT4p9\r\ncreating /tmp/tmpauT4p9/tmp/tmpauT4p9/src.linux-x86_64-2.7\r\ncompile options: '-I/tmp/tmpauT4p9/src.linux-x86_64-2.7 -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c'\r\nx86_64-linux-gnu-gcc: /tmp/tmpauT4p9/src.linux-x86_64-2.7/fortranobject.c\r\nIn file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1761:0,\r\n                 from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:17,\r\n                 from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,\r\n                 from /tmp/tmpauT4p9/src.linux-x86_64-2.7/fortranobject.h:13,\r\n                 from /tmp/tmpauT4p9/src.linux-x86_64-2.7/fortranobject.c:2:\r\n/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning \"Using deprecated NumPy API, disable it by \" \"#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION\" [-Wcpp]\r\n #warning \"Using deprecated NumPy API, disable it by \" \\\r\n  ^\r\nx86_64-linux-gnu-gcc: /tmp/tmpauT4p9/src.linux-x86_64-2.7/f2py_selected_kindmodule.c\r\nIn file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1761:0,\r\n                 from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:17,\r\n                 from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,\r\n                 from /tmp/tmpauT4p9/src.linux-x86_64-2.7/fortranobject.h:13,\r\n                 from /tmp/tmpauT4p9/src.linux-x86_64-2.7/f2py_selected_kindmodule.c:17:\r\n/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning \"Using deprecated NumPy API, disable it by \" \"#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION\" [-Wcpp]\r\n #warning \"Using deprecated NumPy API, disable it by \" \\\r\n  ^\r\ncompiling Fortran 90 module sources\r\nFortran f77 compiler: /usr/bin/gfortran -Wall -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops\r\nFortran f90 compiler: /usr/bin/gfortran -Wall -fno-second-underscore -fPIC -O3 -funroll-loops\r\nFortran fix compiler: /usr/bin/gfortran -Wall -ffixed-form -fno-second-underscore -Wall -fno-second-underscore -fPIC -O3 -funroll-loops\r\ncompile options: '-I/tmp/tmpauT4p9/src.linux-x86_64-2.7 -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c'\r\nextra options: '-J/tmp/tmpauT4p9/ -I/tmp/tmpauT4p9/'\r\ngfortran:f90: f2py_selected_kind.f90\r\ncompiling Fortran sources\r\nFortran f77 compiler: /usr/bin/gfortran -Wall -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops\r\nFortran f90 compiler: /usr/bin/gfortran -Wall -fno-second-underscore -fPIC -O3 -funroll-loops\r\nFortran fix compiler: /usr/bin/gfortran -Wall -ffixed-form -fno-second-underscore -Wall -fno-second-underscore -fPIC -O3 -funroll-loops\r\ncompile options: '-I/tmp/tmpauT4p9/src.linux-x86_64-2.7 -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c'\r\nextra options: '-J/tmp/tmpauT4p9/ -I/tmp/tmpauT4p9/'\r\ngfortran:f90: /tmp/tmpauT4p9/src.linux-x86_64-2.7/f2py_selected_kind-f2pywrappers2.f90\r\n/usr/bin/gfortran -Wall -Wall -shared /tmp/tmpauT4p9/tmp/tmpauT4p9/src.linux-x86_64-2.7/f2py_selected_kindmodule.o /tmp/tmpauT4p9/tmp/tmpauT4p9/src.linux-x86_64-2.7/fortranobject.o /tmp/tmpauT4p9/f2py_selected_kind.o /tmp/tmpauT4p9/tmp/tmpauT4p9/src.linux-x86_64-2.7/f2py_selected_kind-f2pywrappers2.o -lgfortran -o ./f2py_selected_kind.so\r\nRemoving build directory /tmp/tmpauT4p9\r\n['-c', '-c', '--fcompiler=gnu95', '--f90flags=\"-ffree-line-length-none -ffree-form -xf95-cpp-input -Wall -O3 -fimplicit-none\"', '-m', 'kmc_model', 'kind_values_f2py.f90', 'base.f90', 'lattice.f90', 'proclist.f90']\r\nrunning build\r\nrunning config_cc\r\nunifing config_cc, config, build_clib, build_ext, build commands --compiler options\r\nrunning config_fc\r\nunifing config_fc, config, build_clib, build_ext, build commands --fcompiler options\r\nrunning build_src\r\nbuild_src\r\nbuilding extension \"kmc_model\" sources\r\nf2py options: []\r\nf2py:> /tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_modelmodule.c\r\ncreating /tmp/tmpOUPHrs/src.linux-x86_64-2.7\r\nReading fortran codes...\r\n\tReading file 'kind_values_f2py.f90' (format:free)\r\n\tReading file 'base.f90' (format:free)\r\nrmbadname1: Replacing \"switch\" with \"switch_bn\".\r\nrmbadname1: Replacing \"switch\" with \"switch_bn\".\r\n\tReading file 'lattice.f90' (format:free)\r\n\tReading file 'proclist.f90' (format:free)\r\nPost-processing...\r\n\tBlock: kmc_model\r\n\t\t\tBlock: kind_values\r\n\t\t\tBlock: base\r\n\t\t\t\tBlock: del_proc\r\n\t\t\t\tBlock: add_proc\r\n\t\t\t\tBlock: can_do\r\nIn: :kmc_model:base.f90:base:can_do\r\nanalyzevars: prefix ('pure') were not used\r\n\t\t\t\tBlock: reset_site\r\n\t\t\t\tBlock: reload_system\r\n\t\t\t\tBlock: save_system\r\n\t\t\t\tBlock: set_rate_const\r\n\t\t\t\tBlock: update_accum_rate\r\n\t\t\t\tBlock: update_integ_rate\r\n\t\t\t\tBlock: allocate_system\r\n\t\t\t\tBlock: is_allocated\r\n\t\t\t\tBlock: deallocate_system\r\n\t\t\t\tBlock: get_system_name\r\nIn: :kmc_model:base.f90:base:get_system_name\r\nanalyzevars: prefix ('pure') were not used\r\n\t\t\t\tBlock: set_system_name\r\n\t\t\t\tBlock: set_kmc_time\r\n\t\t\t\tBlock: get_kmc_time\r\n\t\t\t\tBlock: get_kmc_time_step\r\n\t\t\t\tBlock: get_procstat\r\n\t\t\t\tBlock: get_nrofsites\r\n\t\t\t\tBlock: get_avail_site\r\n\t\t\t\tBlock: get_accum_rate\r\n\t\t\t\tBlock: get_integ_rate\r\n\t\t\t\tBlock: get_rate\r\n\t\t\t\tBlock: increment_procstat\r\n\t\t\t\tBlock: get_walltime\r\n\t\t\t\tBlock: get_volume\r\n\t\t\t\tBlock: get_kmc_step\r\n\t\t\t\tBlock: determine_procsite\r\n\t\t\t\tBlock: update_clocks\r\n\t\t\t\tBlock: get_species\r\nIn: :kmc_model:base.f90:base:get_species\r\nanalyzevars: prefix ('pure') were not used\r\n\t\t\t\tBlock: replace_species\r\n\t\t\t\tBlock: interval_search_real\r\n\t\t\t\tBlock: assertion_fail\r\n\t\t\t\tBlock: set_null_species\r\n\t\t\t\tBlock: get_null_species\r\n\t\t\tBlock: lattice\r\n\t\t\t\tBlock: calculate_lattice2nr\r\nIn: :kmc_model:lattice.f90:lattice:calculate_lattice2nr\r\nanalyzevars: prefix ('pure') were not used\r\n\t\t\t\tBlock: calculate_nr2lattice\r\nIn: :kmc_model:lattice.f90:lattice:calculate_nr2lattice\r\nanalyzevars: prefix ('pure') were not used\r\n\t\t\t\tBlock: allocate_system\r\n\t\t\t\tBlock: deallocate_system\r\n\t\t\t\tBlock: add_proc\r\n\t\t\t\tBlock: del_proc\r\n\t\t\t\tBlock: can_do\r\nIn: :kmc_model:lattice.f90:lattice:can_do\r\nanalyzevars: prefix ('pure') were not used\r\n\t\t\t\tBlock: replace_species\r\n\t\t\t\tBlock: get_species\r\nIn: :kmc_model:lattice.f90:lattice:get_species\r\nanalyzevars: prefix ('pure') were not used\r\n\t\t\t\tBlock: reset_site\r\n\t\t\tBlock: proclist\r\nget_useparameters: mapping for {'map': {'lattice2nr': 'lattice2nr', 'add_proc': 'add_proc', 'replace_species': 'replace_species', 'system_size': 'system_size', 'del_proc': 'del_proc', 'set_rate_const': 'set_rate_const', 'can_do': 'can_do', 'simple_cubic': 'simple_cubic', 'simple_cubic_hollow': 'simple_cubic_hollow', 'reset_site': 'reset_site', 'spuck': 'spuck', 'nr2lattice': 'nr2lattice', 'allocate_system': 'allocate_system', 'get_species': 'get_species'}, 'only': 1} not impl.\t\t\t\tBlock: do_kmc_steps\r\nget_useparameters: mapping for {'map': {'lattice2nr': 'lattice2nr', 'add_proc': 'add_proc', 'replace_species': 'replace_species', 'system_size': 'system_size', 'del_proc': 'del_proc', 'set_rate_const': 'set_rate_const', 'can_do': 'can_do', 'simple_cubic': 'simple_cubic', 'simple_cubic_hollow': 'simple_cubic_hollow', 'reset_site': 'reset_site', 'spuck': 'spuck', 'nr2lattice': 'nr2lattice', 'allocate_system': 'allocate_system', 'get_species': 'get_species'}, 'only': 1} not impl.\t\t\t\tBlock: do_kmc_step\r\nget_useparameters: mapping for {'map': {'lattice2nr': 'lattice2nr', 'add_proc': 'add_proc', 'replace_species': 'replace_species', 'system_size': 'system_size', 'del_proc': 'del_proc', 'set_rate_const': 'set_rate_const', 'can_do': 'can_do', 'simple_cubic': 'simple_cubic', 'simple_cubic_hollow': 'simple_cubic_hollow', 'reset_site': 'reset_site', 'spuck': 'spuck', 'nr2lattice': 'nr2lattice', 'allocate_system': 'allocate_system', 'get_species': 'get_species'}, 'only': 1} not impl.\t\t\t\tBlock: get_next_kmc_step\r\nget_useparameters: mapping for {'map': {'lattice2nr': 'lattice2nr', 'add_proc': 'add_proc', 'replace_species': 'replace_species', 'system_size': 'system_size', 'del_proc': 'del_proc', 'set_rate_const': 'set_rate_const', 'can_do': 'can_do', 'simple_cubic': 'simple_cubic', 'simple_cubic_hollow': 'simple_cubic_hollow', 'reset_site': 'reset_site', 'spuck': 'spuck', 'nr2lattice': 'nr2lattice', 'allocate_system': 'allocate_system', 'get_species': 'get_species'}, 'only': 1} not impl.\t\t\t\tBlock: get_occupation\r\nget_useparameters: mapping for {'map': {'lattice2nr': 'lattice2nr', 'add_proc': 'add_proc', 'replace_species': 'replace_species', 'system_size': 'system_size', 'del_proc': 'del_proc', 'set_rate_const': 'set_rate_const', 'can_do': 'can_do', 'simple_cubic': 'simple_cubic', 'simple_cubic_hollow': 'simple_cubic_hollow', 'reset_site': 'reset_site', 'spuck': 'spuck', 'nr2lattice': 'nr2lattice', 'allocate_system': 'allocate_system', 'get_species': 'get_species'}, 'only': 1} not impl.\t\t\t\tBlock: init\r\nget_useparameters: mapping for {'map': {'lattice2nr': 'lattice2nr', 'add_proc': 'add_proc', 'replace_species': 'replace_species', 'system_size': 'system_size', 'del_proc': 'del_proc', 'set_rate_const': 'set_rate_const', 'can_do': 'can_do', 'simple_cubic': 'simple_cubic', 'simple_cubic_hollow': 'simple_cubic_hollow', 'reset_site': 'reset_site', 'spuck': 'spuck', 'nr2lattice': 'nr2lattice', 'allocate_system': 'allocate_system', 'get_species': 'get_species'}, 'only': 1} not impl.\t\t\t\tBlock: initialize_state\r\nget_useparameters: mapping for {'map': {'lattice2nr': 'lattice2nr', 'add_proc': 'add_proc', 'replace_species': 'replace_species', 'system_size': 'system_size', 'del_proc': 'del_proc', 'set_rate_const': 'set_rate_const', 'can_do': 'can_do', 'simple_cubic': 'simple_cubic', 'simple_cubic_hollow': 'simple_cubic_hollow', 'reset_site': 'reset_site', 'spuck': 'spuck', 'nr2lattice': 'nr2lattice', 'allocate_system': 'allocate_system', 'get_species': 'get_species'}, 'only': 1} not impl.\t\t\t\tBlock: run_proc_nr\r\nget_useparameters: mapping for {'map': {'lattice2nr': 'lattice2nr', 'add_proc': 'add_proc', 'replace_species': 'replace_species', 'system_size': 'system_size', 'del_proc': 'del_proc', 'set_rate_const': 'set_rate_const', 'can_do': 'can_do', 'simple_cubic': 'simple_cubic', 'simple_cubic_hollow': 'simple_cubic_hollow', 'reset_site': 'reset_site', 'spuck': 'spuck', 'nr2lattice': 'nr2lattice', 'allocate_system': 'allocate_system', 'get_species': 'get_species'}, 'only': 1} not impl.\t\t\t\tBlock: put_co_simple_cubic_hollow\r\nget_useparameters: mapping for {'map': {'lattice2nr': 'lattice2nr', 'add_proc': 'add_proc', 'replace_species': 'replace_species', 'system_size': 'system_size', 'del_proc': 'del_proc', 'set_rate_const': 'set_rate_const', 'can_do': 'can_do', 'simple_cubic': 'simple_cubic', 'simple_cubic_hollow': 'simple_cubic_hollow', 'reset_site': 'reset_site', 'spuck': 'spuck', 'nr2lattice': 'nr2lattice', 'allocate_system': 'allocate_system', 'get_species': 'get_species'}, 'only': 1} not impl.\t\t\t\tBlock: take_co_simple_cubic_hollow\r\nget_useparameters: mapping for {'map': {'lattice2nr': 'lattice2nr', 'add_proc': 'add_proc', 'replace_species': 'replace_species', 'system_size': 'system_size', 'del_proc': 'del_proc', 'set_rate_const': 'set_rate_const', 'can_do': 'can_do', 'simple_cubic': 'simple_cubic', 'simple_cubic_hollow': 'simple_cubic_hollow', 'reset_site': 'reset_site', 'spuck': 'spuck', 'nr2lattice': 'nr2lattice', 'allocate_system': 'allocate_system', 'get_species': 'get_species'}, 'only': 1} not impl.\t\t\t\tBlock: touchup_simple_cubic_hollow\r\nget_useparameters: mapping for {'map': {'lattice2nr': 'lattice2nr', 'add_proc': 'add_proc', 'replace_species': 'replace_species', 'system_size': 'system_size', 'del_proc': 'del_proc', 'set_rate_const': 'set_rate_const', 'can_do': 'can_do', 'simple_cubic': 'simple_cubic', 'simple_cubic_hollow': 'simple_cubic_hollow', 'reset_site': 'reset_site', 'spuck': 'spuck', 'nr2lattice': 'nr2lattice', 'allocate_system': 'allocate_system', 'get_species': 'get_species'}, 'only': 1} not impl.Post-processing (stage 2)...\r\n\tBlock: kmc_model\r\n\t\tBlock: unknown_interface\r\n\t\t\tBlock: kind_values\r\n\t\t\tBlock: base\r\n\t\t\t\tBlock: del_proc\r\n\t\t\t\tBlock: add_proc\r\n\t\t\t\tBlock: can_do\r\n\t\t\t\tBlock: reset_site\r\n\t\t\t\tBlock: reload_system\r\n\t\t\t\tBlock: save_system\r\n\t\t\t\tBlock: set_rate_const\r\n\t\t\t\tBlock: update_accum_rate\r\n\t\t\t\tBlock: update_integ_rate\r\n\t\t\t\tBlock: allocate_system\r\n\t\t\t\tBlock: is_allocated\r\n\t\t\t\tBlock: deallocate_system\r\n\t\t\t\tBlock: get_system_name\r\n\t\t\t\tBlock: set_system_name\r\n\t\t\t\tBlock: set_kmc_time\r\n\t\t\t\tBlock: get_kmc_time\r\n\t\t\t\tBlock: get_kmc_time_step\r\n\t\t\t\tBlock: get_procstat\r\n\t\t\t\tBlock: get_nrofsites\r\n\t\t\t\tBlock: get_avail_site\r\n\t\t\t\tBlock: get_accum_rate\r\n\t\t\t\tBlock: get_integ_rate\r\n\t\t\t\tBlock: get_rate\r\n\t\t\t\tBlock: increment_procstat\r\n\t\t\t\tBlock: get_walltime\r\n\t\t\t\tBlock: get_volume\r\n\t\t\t\tBlock: get_kmc_step\r\n\t\t\t\tBlock: determine_procsite\r\n\t\t\t\tBlock: update_clocks\r\n\t\t\t\tBlock: get_species\r\n\t\t\t\tBlock: replace_species\r\n\t\t\t\tBlock: interval_search_real\r\n\t\t\t\tBlock: assertion_fail\r\n\t\t\t\tBlock: set_null_species\r\n\t\t\t\tBlock: get_null_species\r\n\t\t\tBlock: lattice\r\n\t\t\t\tBlock: calculate_lattice2nr\r\n\t\t\t\tBlock: calculate_nr2lattice\r\n\t\t\t\tBlock: allocate_system\r\n\t\t\t\tBlock: deallocate_system\r\n\t\t\t\tBlock: add_proc\r\n\t\t\t\tBlock: del_proc\r\n\t\t\t\tBlock: can_do\r\n\t\t\t\tBlock: replace_species\r\n\t\t\t\tBlock: get_species\r\n\t\t\t\tBlock: reset_site\r\n\t\t\tBlock: proclist\r\n\t\t\t\tBlock: do_kmc_steps\r\n\t\t\t\tBlock: do_kmc_step\r\n\t\t\t\tBlock: get_next_kmc_step\r\n\t\t\t\tBlock: get_occupation\r\n\t\t\t\tBlock: init\r\n\t\t\t\tBlock: initialize_state\r\n\t\t\t\tBlock: run_proc_nr\r\n\t\t\t\tBlock: put_co_simple_cubic_hollow\r\n\t\t\t\tBlock: take_co_simple_cubic_hollow\r\n\t\t\t\tBlock: touchup_simple_cubic_hollow\r\nBuilding modules...\r\n\tBuilding module \"kmc_model\"...\r\n\t\tConstructing F90 module support for \"kind_values\"...\r\n\t\t  Variables: ilong ibyte iint rsingle rdouble ishort\r\n\t\tConstructing F90 module support for \"base\"...\r\n\t\t\tConstructing wrapper function \"base.del_proc\"...\r\n\t\t\t  del_proc(proc,site)\r\n\t\t\tConstructing wrapper function \"base.add_proc\"...\r\n\t\t\t  add_proc(proc,site)\r\n\t\tCreating wrapper for Fortran function \"can_do\"(\"can_do\")...\r\n\t\t\tConstructing wrapper function \"base.can_do\"...\r\n\t\t\t  can_do = can_do(proc,site)\r\n\t\t\tConstructing wrapper function \"base.reset_site\"...\r\n\t\t\t  reset_site(site,old_species)\r\n\t\t\tConstructing wrapper function \"base.reload_system\"...\r\n\t\t\t  reloaded = reload_system(input_system_name)\r\n\t\t\tConstructing wrapper function \"base.save_system\"...\r\n\t\t\t  save_system()\r\n\t\t\tConstructing wrapper function \"base.set_rate_const\"...\r\n\t\t\t  set_rate_const(proc_nr,rate)\r\n\t\t\tConstructing wrapper function \"base.update_accum_rate\"...\r\n\t\t\t  update_accum_rate()\r\n\t\t\tConstructing wrapper function \"base.update_integ_rate\"...\r\n\t\t\t  update_integ_rate()\r\n\t\t\tConstructing wrapper function \"base.allocate_system\"...\r\n\t\t\t  allocate_system(input_nr_of_proc,input_volume,input_system_name)\r\n\t\t\tConstructing wrapper function \"base.is_allocated\"...\r\n\t\t\t  result = is_allocated()\r\n\t\t\tConstructing wrapper function \"base.deallocate_system\"...\r\n\t\t\t  deallocate_system()\r\n\t\tCreating wrapper for Fortran function \"get_system_name\"(\"get_system_name\")...\r\n\t\t\tConstructing wrapper function \"base.get_system_name\"...\r\n\t\t\t  get_system_name = get_system_name()\r\n\t\t\tConstructing wrapper function \"base.set_system_name\"...\r\n\t\t\t  set_system_name(input_system_name)\r\n\t\t\tConstructing wrapper function \"base.set_kmc_time\"...\r\n\t\t\t  set_kmc_time(new_kmc_time)\r\n\t\t\tConstructing wrapper function \"base.get_kmc_time\"...\r\n\t\t\t  return_kmc_time = get_kmc_time()\r\n\t\t\tConstructing wrapper function \"base.get_kmc_time_step\"...\r\n\t\t\t  return_kmc_time_step = get_kmc_time_step()\r\n\t\t\tConstructing wrapper function \"base.get_procstat\"...\r\n\t\t\t  return_procstat = get_procstat(proc)\r\n\t\t\tConstructing wrapper function \"base.get_nrofsites\"...\r\n\t\t\t  return_nrofsites = get_nrofsites(proc)\r\n\t\t\tConstructing wrapper function \"base.get_avail_site\"...\r\n\t\t\t  return_avail_site = get_avail_site(proc_nr,field,switch_bn)\r\n\t\t\tConstructing wrapper function \"base.get_accum_rate\"...\r\n\t\t\t  return_accum_rate = get_accum_rate([proc_nr])\r\n\t\t\tConstructing wrapper function \"base.get_integ_rate\"...\r\n\t\t\t  return_integ_rate = get_integ_rate([proc_nr])\r\n\t\t\tConstructing wrapper function \"base.get_rate\"...\r\n\t\t\t  return_rate = get_rate(proc_nr)\r\n\t\t\tConstructing wrapper function \"base.increment_procstat\"...\r\n\t\t\t  increment_procstat(proc)\r\n\t\t\tConstructing wrapper function \"base.get_walltime\"...\r\n\t\t\t  return_walltime = get_walltime()\r\n\t\t\tConstructing wrapper function \"base.get_volume\"...\r\n\t\t\t  return_volume = get_volume()\r\n\t\t\tConstructing wrapper function \"base.get_kmc_step\"...\r\n\t\t\t  return_kmc_step = get_kmc_step()\r\n\t\t\tConstructing wrapper function \"base.determine_procsite\"...\r\n\t\t\t  proc,site = determine_procsite(ran_proc,ran_site)\r\n\t\t\tConstructing wrapper function \"base.update_clocks\"...\r\n\t\t\t  update_clocks(ran_time)\r\n\t\tCreating wrapper for Fortran function \"get_species\"(\"get_species\")...\r\n\t\t\tConstructing wrapper function \"base.get_species\"...\r\n\t\t\t  get_species = get_species(site)\r\n\t\t\tConstructing wrapper function \"base.replace_species\"...\r\n\t\t\t  replace_species(site,old_species,new_species)\r\n\t\tCreating wrapper for Fortran subroutine \"interval_search_real\"(\"interval_search_real\")...\r\n\t\t\tConstructing wrapper function \"base.interval_search_real\"...\r\n\t\t\t  return_field = interval_search_real(arr,value)\r\n\t\t\tConstructing wrapper function \"base.assertion_fail\"...\r\n\t\t\t  assertion_fail(a,r)\r\n\t\t\tConstructing wrapper function \"base.set_null_species\"...\r\n\t\t\t  set_null_species(input_null_species)\r\n\t\t\tConstructing wrapper function \"base.get_null_species\"...\r\n\t\t\t  output_null_species = get_null_species()\r\n\t\tConstructing F90 module support for \"lattice\"...\r\n\t\t  Variables: substrate_layer site_positions nr_of_layers system_size model_dimension simple_cubic simple_cubic_hollow default_layer unit_cell_size nr2lattice lattice2nr spuck\r\ngetarrdims:warning: assumed shape array, using 0 instead of ':'\r\ngetarrdims:warning: assumed shape array, using 0 instead of ':'\r\ngetarrdims:warning: assumed shape array, using 0 instead of ':'\r\ngetarrdims:warning: assumed shape array, using 0 instead of ':'\r\ngetarrdims:warning: assumed shape array, using 0 instead of ':'\r\ngetarrdims:warning: assumed shape array, using 0 instead of ':'\r\n\t\tCreating wrapper for Fortran function \"calculate_lattice2nr\"(\"calculate_lattice2nr\")...\r\n\t\t\tConstructing wrapper function \"lattice.calculate_lattice2nr\"...\r\n\t\t\t  calculate_lattice2nr = calculate_lattice2nr(site)\r\n\t\tCreating wrapper for Fortran function \"calculate_nr2lattice\"(\"calculate_nr2lattice\")...\r\n\t\t\tConstructing wrapper function \"lattice.calculate_nr2lattice\"...\r\n\t\t\t  calculate_nr2lattice = calculate_nr2lattice(nr)\r\n\t\t\tConstructing wrapper function \"lattice.allocate_system\"...\r\n\t\t\t  allocate_system(nr_of_proc,input_system_size,system_name)\r\n\t\t\tConstructing wrapper function \"lattice.deallocate_system\"...\r\n\t\t\t  deallocate_system()\r\n\t\t\tConstructing wrapper function \"lattice.add_proc\"...\r\n\t\t\t  add_proc(proc,site)\r\n\t\t\tConstructing wrapper function \"lattice.del_proc\"...\r\n\t\t\t  del_proc(proc,site)\r\n\t\tCreating wrapper for Fortran function \"can_do\"(\"can_do\")...\r\n\t\t\tConstructing wrapper function \"lattice.can_do\"...\r\n\t\t\t  can_do = can_do(proc,site)\r\n\t\t\tConstructing wrapper function \"lattice.replace_species\"...\r\n\t\t\t  replace_species(site,old_species,new_species)\r\n\t\tCreating wrapper for Fortran function \"get_species\"(\"get_species\")...\r\n\t\t\tConstructing wrapper function \"lattice.get_species\"...\r\n\t\t\t  get_species = get_species(site)\r\n\t\t\tConstructing wrapper function \"lattice.reset_site\"...\r\n\t\t\t  reset_site(site,old_species)\r\n\t\tConstructing F90 module support for \"proclist\"...\r\n\t\t  Variables: co seed_arr default_species seed_size nr_of_species nr_of_proc seed co_adsorption co_desorption representation_length empty\r\ngetarrdims:warning: assumed shape array, using 0 instead of ':'\r\n\t\t\tConstructing wrapper function \"proclist.do_kmc_steps\"...\r\n\t\t\t  do_kmc_steps(n)\r\n\t\t\tConstructing wrapper function \"proclist.do_kmc_step\"...\r\n\t\t\t  do_kmc_step()\r\n\t\t\tConstructing wrapper function \"proclist.get_next_kmc_step\"...\r\n\t\t\t  proc_nr,nr_site = get_next_kmc_step()\r\n\t\t\tConstructing wrapper function \"proclist.get_occupation\"...\r\n\t\t\t  occupation = get_occupation()\r\n\t\t\tConstructing wrapper function \"proclist.init\"...\r\n\t\t\t  init(input_system_size,system_name,layer,seed_in,[no_banner])\r\n\t\t\tConstructing wrapper function \"proclist.initialize_state\"...\r\n\t\t\t  initialize_state(layer,seed_in)\r\n\t\t\tConstructing wrapper function \"proclist.run_proc_nr\"...\r\n\t\t\t  run_proc_nr(proc,nr_site)\r\n\t\t\tConstructing wrapper function \"proclist.put_co_simple_cubic_hollow\"...\r\n\t\t\t  put_co_simple_cubic_hollow(site)\r\n\t\t\tConstructing wrapper function \"proclist.take_co_simple_cubic_hollow\"...\r\n\t\t\t  take_co_simple_cubic_hollow(site)\r\n\t\t\tConstructing wrapper function \"proclist.touchup_simple_cubic_hollow\"...\r\n\t\t\t  touchup_simple_cubic_hollow(site)\r\n\tWrote C/API module \"kmc_model\" to file \"/tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_modelmodule.c\"\r\n\tFortran 90 wrappers are saved to \"/tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_model-f2pywrappers2.f90\"\r\n  adding '/tmp/tmpOUPHrs/src.linux-x86_64-2.7/fortranobject.c' to sources.\r\n  adding '/tmp/tmpOUPHrs/src.linux-x86_64-2.7' to include_dirs.\r\ncopying /usr/lib/python2.7/dist-packages/numpy/f2py/src/fortranobject.c -> /tmp/tmpOUPHrs/src.linux-x86_64-2.7\r\ncopying /usr/lib/python2.7/dist-packages/numpy/f2py/src/fortranobject.h -> /tmp/tmpOUPHrs/src.linux-x86_64-2.7\r\n  adding '/tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_model-f2pywrappers2.f90' to sources.\r\nbuild_src: building npy-pkg config files\r\nrunning build_ext\r\ncustomize UnixCCompiler\r\ncustomize UnixCCompiler using build_ext\r\ncustomize Gnu95FCompiler\r\ncustomize Gnu95FCompiler using build_ext\r\nbuilding 'kmc_model' extension\r\ncompiling C sources\r\nC compiler: x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC\r\n\r\ncreating /tmp/tmpOUPHrs/tmp\r\ncreating /tmp/tmpOUPHrs/tmp/tmpOUPHrs\r\ncreating /tmp/tmpOUPHrs/tmp/tmpOUPHrs/src.linux-x86_64-2.7\r\ncompile options: '-I/tmp/tmpOUPHrs/src.linux-x86_64-2.7 -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c'\r\nx86_64-linux-gnu-gcc: /tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_modelmodule.c\r\nIn file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1761:0,\r\n                 from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:17,\r\n                 from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,\r\n                 from /tmp/tmpOUPHrs/src.linux-x86_64-2.7/fortranobject.h:13,\r\n                 from /tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_modelmodule.c:18:\r\n/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning \"Using deprecated NumPy API, disable it by \" \"#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION\" [-Wcpp]\r\n #warning \"Using deprecated NumPy API, disable it by \" \\\r\n  ^\r\n/tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_modelmodule.c: In function ‘f2py_setup_lattice’:\r\n/tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_modelmodule.c:4699:35: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]\r\n   f2py_lattice_def[i_f2py++].func = nr2lattice;\r\n                                   ^\r\n/tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_modelmodule.c:4700:35: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]\r\n   f2py_lattice_def[i_f2py++].func = lattice2nr;\r\n                                   ^\r\n/tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_modelmodule.c: In function ‘f2py_setup_proclist’:\r\n/tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_modelmodule.c:4747:36: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]\r\n   f2py_proclist_def[i_f2py++].func = seed_arr;\r\n                                    ^\r\n/tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_modelmodule.c: At top level:\r\n/tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_modelmodule.c:144:12: warning: ‘f2py_size’ defined but not used [-Wunused-function]\r\n static int f2py_size(PyArrayObject* var, ...)\r\n            ^\r\nx86_64-linux-gnu-gcc: /tmp/tmpOUPHrs/src.linux-x86_64-2.7/fortranobject.c\r\nIn file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1761:0,\r\n                 from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:17,\r\n                 from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,\r\n                 from /tmp/tmpOUPHrs/src.linux-x86_64-2.7/fortranobject.h:13,\r\n                 from /tmp/tmpOUPHrs/src.linux-x86_64-2.7/fortranobject.c:2:\r\n/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning \"Using deprecated NumPy API, disable it by \" \"#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION\" [-Wcpp]\r\n #warning \"Using deprecated NumPy API, disable it by \" \\\r\n  ^\r\ncompiling Fortran 90 module sources\r\nFortran f77 compiler: /usr/bin/gfortran -Wall -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops\r\nFortran f90 compiler: /usr/bin/gfortran -ffree-line-length-none -ffree-form -xf95-cpp-input -Wall -O3 -fimplicit-none -fPIC -O3 -funroll-loops\r\nFortran fix compiler: /usr/bin/gfortran -Wall -ffixed-form -fno-second-underscore -ffree-line-length-none -ffree-form -xf95-cpp-input -Wall -O3 -fimplicit-none -fPIC -O3 -funroll-loops\r\ncompile options: '-I/tmp/tmpOUPHrs/src.linux-x86_64-2.7 -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c'\r\nextra options: '-J/tmp/tmpOUPHrs/ -I/tmp/tmpOUPHrs/'\r\ngfortran:f90: kind_values_f2py.f90\r\ngfortran:f90: base.f90\r\ngfortran:f90: lattice.f90\r\ngfortran:f90: proclist.f90\r\ncompiling Fortran sources\r\nFortran f77 compiler: /usr/bin/gfortran -Wall -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops\r\nFortran f90 compiler: /usr/bin/gfortran -ffree-line-length-none -ffree-form -xf95-cpp-input -Wall -O3 -fimplicit-none -fPIC -O3 -funroll-loops\r\nFortran fix compiler: /usr/bin/gfortran -Wall -ffixed-form -fno-second-underscore -ffree-line-length-none -ffree-form -xf95-cpp-input -Wall -O3 -fimplicit-none -fPIC -O3 -funroll-loops\r\ncompile options: '-I/tmp/tmpOUPHrs/src.linux-x86_64-2.7 -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c'\r\nextra options: '-J/tmp/tmpOUPHrs/ -I/tmp/tmpOUPHrs/'\r\ngfortran:f90: /tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_model-f2pywrappers2.f90\r\n/tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_model-f2pywrappers2.f90:122:19:\r\n\r\n       integer r,i,j\r\n                   1\r\nWarning: Unused variable ‘j’ declared at (1) [-Wunused-variable]\r\n/tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_model-f2pywrappers2.f90:152:19:\r\n\r\n       integer r,i,j\r\n                   1\r\nWarning: Unused variable ‘j’ declared at (1) [-Wunused-variable]\r\n/tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_model-f2pywrappers2.f90:206:10:\r\n\r\n       use lattice, only : substrate_layer\r\n          1\r\nWarning: Unused module variable ‘lattice2nr’ which has been explicitly imported at (1) [-Wunused-variable]\r\n/tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_model-f2pywrappers2.f90:206:10:\r\n\r\n       use lattice, only : substrate_layer\r\n          1\r\nWarning: Unused module variable ‘nr2lattice’ which has been explicitly imported at (1) [-Wunused-variable]\r\n/tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_model-f2pywrappers2.f90:269:19:\r\n\r\n       integer r,i,j\r\n                   1\r\nWarning: Unused variable ‘j’ declared at (1) [-Wunused-variable]\r\n/tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_model-f2pywrappers2.f90:295:10:\r\n\r\n       use proclist, only : co\r\n          1\r\nWarning: Unused module variable ‘seed_arr’ which has been explicitly imported at (1) [-Wunused-variable]\r\n/usr/bin/gfortran -Wall -Wall -shared /tmp/tmpOUPHrs/tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_modelmodule.o /tmp/tmpOUPHrs/tmp/tmpOUPHrs/src.linux-x86_64-2.7/fortranobject.o /tmp/tmpOUPHrs/kind_values_f2py.o /tmp/tmpOUPHrs/base.o /tmp/tmpOUPHrs/lattice.o /tmp/tmpOUPHrs/proclist.o /tmp/tmpOUPHrs/tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_model-f2pywrappers2.o -lgfortran -o ./kmc_model.so\r\nRemoving build directory /tmp/tmpOUPHrs\r\n`\r\n"}}