jiangwangzhangs
commented
8 years ago I run the code again and it is OK ! thanks!
Closed jiangwangzhangs closed 8 years ago
jiangwangzhangs
commented
8 years ago I run the code again and it is OK ! thanks!
thank u for ur help yesterday, mhoffman. After following the instructions, everything seems OK. And I wait for the result, but after over10 hours, the kmos is still running!! Is there any problems with my fisrtmodel?
`In [1]: from kmos.types import *
In [2]: from kmos.io import *
In [3]: import numpy as np
In [4]: os.getcwd() Out[4]: '/home/jiangzhen'
In [5]: pt = Project()
In [6]: pt.set_meta(author = 'Your Name', ...: email = 'your.name@server.com', ...: model_name = 'MyFirstModel', ...: model_dimension = 2,)
In [7]: pt.add_species(name='empty') Out[7]: [SPECIES] Name: empty Color: no color set.
In [8]: pt.add_species(name='CO', ...: representation="Atoms('CO',[[0,0,0],[0,0,1.2]])") Out[8]: [SPECIES] Name: CO Color: no color set.
In [9]: layer = pt.add_layer(name='simple_cubic')
In [10]: layer.sites.append(Site(name='hollow', pos='0.5 0.5 0.5', ....: default_species='empty'))
In [11]: pt.lattice.cell = np.diag([3.5, 3.5, 10])
In [12]: pt.add_parameter(name='T', value=600., adjustable=True, min=400, max=800) Out[12]: [PARAMETER] Name: T Value: 600.0
In [13]: pt.add_parameter(name='p_CO', value=1., adjustable=True, min=1e-10, max=1.e2) Out[13]: [PARAMETER] Name: p_CO Value: 1.0
In [14]: pt.add_parameter(name='A', value='(3.5_angstrom)__2') Out[14]: [PARAMETER] Name: A Value: (3.5_angstrom)**2
In [15]: pt.add_parameter(name='deltaG', value='-0.5', adjustable=True, ....: min=-1.3, max=0.3) Out[15]: [PARAMETER] Name: deltaG Value: -0.5
In [16]: coord = pt.lattice.generate_coord('hollow.(0,0,0).simple_cubic')
In [17]: pt.add_process(name='CO_adsorption', ....: conditions=[Condition(coord=coord, species='empty')], ....: actions=[Action(coord=coord, species='CO')], ....: rate_constant='p_CO_bar_A/sqrt(2_pi_umass_m_CO/beta)') Out[17]: [PROCESS] Name:CO_adsorption Rate: p_CO_bar_A/sqrt(2_pi_umass_m_CO/beta) Conditions: [[COND_ACT] Species: empty Coord:[COORD] hollow.(0, 0, 0).simple_cubic ] Actions: [[COND_ACT] Species: CO Coord:[COORD] hollow.(0, 0, 0).simple_cubic ]
In [18]: pt.add_process(name='CO_desorption', ....: conditions=[Condition(coord=coord, species='CO')], ....: actions=[Action(coord=coord, species='empty')], ....: rate_constant='p_CO_bar_A/sqrt(2_pi_umass_m_CO/beta)_exp(beta_deltaG_eV)') Out[18]: [PROCESS] Name:CO_desorption Rate: p_CO_bar_A/sqrt(2_pi_umass_m_CO/beta)_exp(beta_deltaG_eV) Conditions: [[COND_ACT] Species: CO Coord:[COORD] hollow.(0, 0, 0).simple_cubic ] Actions: [[COND_ACT] Species: empty Coord:[COORD] hollow.(0, 0, 0).simple_cubic ]
In [19]: pt.filename = 'myfirst_kmc.xml'
In [20]: pt.save()
In [21]: import kmos.cli
In [22]: kmos.cli.main('export myfirst_kmc.xml') No export path provided. Exporting to myfirst_kmc_local_smart /usr/local/lib/python2.7/dist-packages/kmos Unknown vendor: "gfortran" running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src build_src building extension "f2py_selected_kind" sources f2py options: [] f2py:> /tmp/tmpauT4p9/src.linux-x86_64-2.7/f2py_selected_kindmodule.c creating /tmp/tmpauT4p9/src.linux-x86_64-2.7 Reading fortran codes... Reading file 'f2py_selected_kind.f90' (format:free) Post-processing... Block: f2py_selected_kind Block: kind Block: real_kind Block: int_kind Post-processing (stage 2)... Block: f2py_selected_kind Block: unknown_interface Block: kind Block: real_kind Block: int_kind Building modules... Building module "f2py_selected_kind"... Constructing F90 module support for "kind"... Constructing wrapper function "kind.real_kind"... kind_value = real_kind([p,r]) Constructing wrapper function "kind.int_kind"... kind_value = int_kind([p,r]) Wrote C/API module "f2py_selected_kind" to file "/tmp/tmpauT4p9/src.linux-x86_64-2.7/f2py_selected_kindmodule.c" Fortran 90 wrappers are saved to "/tmp/tmpauT4p9/src.linux-x86_64-2.7/f2py_selected_kind-f2pywrappers2.f90" adding '/tmp/tmpauT4p9/src.linux-x86_64-2.7/fortranobject.c' to sources. adding '/tmp/tmpauT4p9/src.linux-x86_64-2.7' to include_dirs. copying /usr/lib/python2.7/dist-packages/numpy/f2py/src/fortranobject.c -> /tmp/tmpauT4p9/src.linux-x86_64-2.7 copying /usr/lib/python2.7/dist-packages/numpy/f2py/src/fortranobject.h -> /tmp/tmpauT4p9/src.linux-x86_64-2.7 adding '/tmp/tmpauT4p9/src.linux-x86_64-2.7/f2py_selected_kind-f2pywrappers2.f90' to sources. build_src: building npy-pkg config files running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize Gnu95FCompiler Found executable /usr/bin/gfortran customize Gnu95FCompiler using build_ext building 'f2py_selected_kind' extension compiling C sources C 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
creating /tmp/tmpauT4p9/tmp creating /tmp/tmpauT4p9/tmp/tmpauT4p9 creating /tmp/tmpauT4p9/tmp/tmpauT4p9/src.linux-x86_64-2.7 compile 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' x86_64-linux-gnu-gcc: /tmp/tmpauT4p9/src.linux-x86_64-2.7/fortranobject.c In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1761:0, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:17, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from /tmp/tmpauT4p9/src.linux-x86_64-2.7/fortranobject.h:13, from /tmp/tmpauT4p9/src.linux-x86_64-2.7/fortranobject.c:2: /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]
warning "Using deprecated NumPy API, disable it by " \
^ x86_64-linux-gnu-gcc: /tmp/tmpauT4p9/src.linux-x86_64-2.7/f2py_selected_kindmodule.c In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1761:0, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:17, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from /tmp/tmpauT4p9/src.linux-x86_64-2.7/fortranobject.h:13, from /tmp/tmpauT4p9/src.linux-x86_64-2.7/f2py_selected_kindmodule.c:17: /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]
warning "Using deprecated NumPy API, disable it by " \
^ compiling Fortran 90 module sources Fortran f77 compiler: /usr/bin/gfortran -Wall -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops Fortran f90 compiler: /usr/bin/gfortran -Wall -fno-second-underscore -fPIC -O3 -funroll-loops Fortran fix compiler: /usr/bin/gfortran -Wall -ffixed-form -fno-second-underscore -Wall -fno-second-underscore -fPIC -O3 -funroll-loops compile 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' extra options: '-J/tmp/tmpauT4p9/ -I/tmp/tmpauT4p9/' gfortran:f90: f2py_selected_kind.f90 compiling Fortran sources Fortran f77 compiler: /usr/bin/gfortran -Wall -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops Fortran f90 compiler: /usr/bin/gfortran -Wall -fno-second-underscore -fPIC -O3 -funroll-loops Fortran fix compiler: /usr/bin/gfortran -Wall -ffixed-form -fno-second-underscore -Wall -fno-second-underscore -fPIC -O3 -funroll-loops compile 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' extra options: '-J/tmp/tmpauT4p9/ -I/tmp/tmpauT4p9/' gfortran:f90: /tmp/tmpauT4p9/src.linux-x86_64-2.7/f2py_selected_kind-f2pywrappers2.f90 /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 Removing build directory /tmp/tmpauT4p9 ['-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'] running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src build_src building extension "kmc_model" sources f2py options: [] f2py:> /tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_modelmodule.c creating /tmp/tmpOUPHrs/src.linux-x86_64-2.7 Reading fortran codes... Reading file 'kind_values_f2py.f90' (format:free) Reading file 'base.f90' (format:free) rmbadname1: Replacing "switch" with "switch_bn". rmbadname1: Replacing "switch" with "switch_bn". Reading file 'lattice.f90' (format:free) Reading file 'proclist.f90' (format:free) Post-processing... Block: kmc_model Block: kind_values Block: base Block: del_proc Block: add_proc Block: can_do In: :kmc_model:base.f90:base:can_do analyzevars: prefix ('pure') were not used Block: reset_site Block: reload_system Block: save_system Block: set_rate_const Block: update_accum_rate Block: update_integ_rate Block: allocate_system Block: is_allocated Block: deallocate_system Block: get_system_name In: :kmc_model:base.f90:base:get_system_name analyzevars: prefix ('pure') were not used Block: set_system_name Block: set_kmc_time Block: get_kmc_time Block: get_kmc_time_step Block: get_procstat Block: get_nrofsites Block: get_avail_site Block: get_accum_rate Block: get_integ_rate Block: get_rate Block: increment_procstat Block: get_walltime Block: get_volume Block: get_kmc_step Block: determine_procsite Block: update_clocks Block: get_species In: :kmc_model:base.f90:base:get_species analyzevars: prefix ('pure') were not used Block: replace_species Block: interval_search_real Block: assertion_fail Block: set_null_species Block: get_null_species Block: lattice Block: calculate_lattice2nr In: :kmc_model:lattice.f90:lattice:calculate_lattice2nr analyzevars: prefix ('pure') were not used Block: calculate_nr2lattice In: :kmc_model:lattice.f90:lattice:calculate_nr2lattice analyzevars: prefix ('pure') were not used Block: allocate_system Block: deallocate_system Block: add_proc Block: del_proc Block: can_do In: :kmc_model:lattice.f90:lattice:can_do analyzevars: prefix ('pure') were not used Block: replace_species Block: get_species In: :kmc_model:lattice.f90:lattice:get_species analyzevars: prefix ('pure') were not used Block: reset_site Block: proclist get_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. Block: do_kmc_steps get_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. Block: do_kmc_step get_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. Block: get_next_kmc_step get_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. Block: get_occupation get_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. Block: init get_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. Block: initialize_state get_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. Block: run_proc_nr get_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. Block: put_co_simple_cubic_hollow get_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. Block: take_co_simple_cubic_hollow get_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. Block: touchup_simple_cubic_hollow get_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)... Block: kmc_model Block: unknown_interface Block: kind_values Block: base Block: del_proc Block: add_proc Block: can_do Block: reset_site Block: reload_system Block: save_system Block: set_rate_const Block: update_accum_rate Block: update_integ_rate Block: allocate_system Block: is_allocated Block: deallocate_system Block: get_system_name Block: set_system_name Block: set_kmc_time Block: get_kmc_time Block: get_kmc_time_step Block: get_procstat Block: get_nrofsites Block: get_avail_site Block: get_accum_rate Block: get_integ_rate Block: get_rate Block: increment_procstat Block: get_walltime Block: get_volume Block: get_kmc_step Block: determine_procsite Block: update_clocks Block: get_species Block: replace_species Block: interval_search_real Block: assertion_fail Block: set_null_species Block: get_null_species Block: lattice Block: calculate_lattice2nr Block: calculate_nr2lattice Block: allocate_system Block: deallocate_system Block: add_proc Block: del_proc Block: can_do Block: replace_species Block: get_species Block: reset_site Block: proclist Block: do_kmc_steps Block: do_kmc_step Block: get_next_kmc_step Block: get_occupation Block: init Block: initialize_state Block: run_proc_nr Block: put_co_simple_cubic_hollow Block: take_co_simple_cubic_hollow Block: touchup_simple_cubic_hollow Building modules... Building module "kmc_model"... Constructing F90 module support for "kind_values"... Variables: ilong ibyte iint rsingle rdouble ishort Constructing F90 module support for "base"... Constructing wrapper function "base.del_proc"... del_proc(proc,site) Constructing wrapper function "base.add_proc"... add_proc(proc,site) Creating wrapper for Fortran function "can_do"("can_do")... Constructing wrapper function "base.can_do"... can_do = can_do(proc,site) Constructing wrapper function "base.reset_site"... reset_site(site,old_species) Constructing wrapper function "base.reload_system"... reloaded = reload_system(input_system_name) Constructing wrapper function "base.save_system"... save_system() Constructing wrapper function "base.set_rate_const"... set_rate_const(proc_nr,rate) Constructing wrapper function "base.update_accum_rate"... update_accum_rate() Constructing wrapper function "base.update_integ_rate"... update_integ_rate() Constructing wrapper function "base.allocate_system"... allocate_system(input_nr_of_proc,input_volume,input_system_name) Constructing wrapper function "base.is_allocated"... result = is_allocated() Constructing wrapper function "base.deallocate_system"... deallocate_system() Creating wrapper for Fortran function "get_system_name"("get_system_name")... Constructing wrapper function "base.get_system_name"... get_system_name = get_system_name() Constructing wrapper function "base.set_system_name"... set_system_name(input_system_name) Constructing wrapper function "base.set_kmc_time"... set_kmc_time(new_kmc_time) Constructing wrapper function "base.get_kmc_time"... return_kmc_time = get_kmc_time() Constructing wrapper function "base.get_kmc_time_step"... return_kmc_time_step = get_kmc_time_step() Constructing wrapper function "base.get_procstat"... return_procstat = get_procstat(proc) Constructing wrapper function "base.get_nrofsites"... return_nrofsites = get_nrofsites(proc) Constructing wrapper function "base.get_avail_site"... return_avail_site = get_avail_site(proc_nr,field,switch_bn) Constructing wrapper function "base.get_accum_rate"... return_accum_rate = get_accum_rate([proc_nr]) Constructing wrapper function "base.get_integ_rate"... return_integ_rate = get_integ_rate([proc_nr]) Constructing wrapper function "base.get_rate"... return_rate = get_rate(proc_nr) Constructing wrapper function "base.increment_procstat"... increment_procstat(proc) Constructing wrapper function "base.get_walltime"... return_walltime = get_walltime() Constructing wrapper function "base.get_volume"... return_volume = get_volume() Constructing wrapper function "base.get_kmc_step"... return_kmc_step = get_kmc_step() Constructing wrapper function "base.determine_procsite"... proc,site = determine_procsite(ran_proc,ran_site) Constructing wrapper function "base.update_clocks"... update_clocks(ran_time) Creating wrapper for Fortran function "get_species"("get_species")... Constructing wrapper function "base.get_species"... get_species = get_species(site) Constructing wrapper function "base.replace_species"... replace_species(site,old_species,new_species) Creating wrapper for Fortran subroutine "interval_search_real"("interval_search_real")... Constructing wrapper function "base.interval_search_real"... return_field = interval_search_real(arr,value) Constructing wrapper function "base.assertion_fail"... assertion_fail(a,r) Constructing wrapper function "base.set_null_species"... set_null_species(input_null_species) Constructing wrapper function "base.get_null_species"... output_null_species = get_null_species() Constructing F90 module support for "lattice"... 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 getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' Creating wrapper for Fortran function "calculate_lattice2nr"("calculate_lattice2nr")... Constructing wrapper function "lattice.calculate_lattice2nr"... calculate_lattice2nr = calculate_lattice2nr(site) Creating wrapper for Fortran function "calculate_nr2lattice"("calculate_nr2lattice")... Constructing wrapper function "lattice.calculate_nr2lattice"... calculate_nr2lattice = calculate_nr2lattice(nr) Constructing wrapper function "lattice.allocate_system"... allocate_system(nr_of_proc,input_system_size,system_name) Constructing wrapper function "lattice.deallocate_system"... deallocate_system() Constructing wrapper function "lattice.add_proc"... add_proc(proc,site) Constructing wrapper function "lattice.del_proc"... del_proc(proc,site) Creating wrapper for Fortran function "can_do"("can_do")... Constructing wrapper function "lattice.can_do"... can_do = can_do(proc,site) Constructing wrapper function "lattice.replace_species"... replace_species(site,old_species,new_species) Creating wrapper for Fortran function "get_species"("get_species")... Constructing wrapper function "lattice.get_species"... get_species = get_species(site) Constructing wrapper function "lattice.reset_site"... reset_site(site,old_species) Constructing F90 module support for "proclist"... Variables: co seed_arr default_species seed_size nr_of_species nr_of_proc seed co_adsorption co_desorption representation_length empty getarrdims:warning: assumed shape array, using 0 instead of ':' Constructing wrapper function "proclist.do_kmc_steps"... do_kmc_steps(n) Constructing wrapper function "proclist.do_kmc_step"... do_kmc_step() Constructing wrapper function "proclist.get_next_kmc_step"... proc_nr,nr_site = get_next_kmc_step() Constructing wrapper function "proclist.get_occupation"... occupation = get_occupation() Constructing wrapper function "proclist.init"... init(input_system_size,system_name,layer,seed_in,[no_banner]) Constructing wrapper function "proclist.initialize_state"... initialize_state(layer,seed_in) Constructing wrapper function "proclist.run_proc_nr"... run_proc_nr(proc,nr_site) Constructing wrapper function "proclist.put_co_simple_cubic_hollow"... put_co_simple_cubic_hollow(site) Constructing wrapper function "proclist.take_co_simple_cubic_hollow"... take_co_simple_cubic_hollow(site) Constructing wrapper function "proclist.touchup_simple_cubic_hollow"... touchup_simple_cubic_hollow(site) Wrote C/API module "kmc_model" to file "/tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_modelmodule.c" Fortran 90 wrappers are saved to "/tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_model-f2pywrappers2.f90" adding '/tmp/tmpOUPHrs/src.linux-x86_64-2.7/fortranobject.c' to sources. adding '/tmp/tmpOUPHrs/src.linux-x86_64-2.7' to include_dirs. copying /usr/lib/python2.7/dist-packages/numpy/f2py/src/fortranobject.c -> /tmp/tmpOUPHrs/src.linux-x86_64-2.7 copying /usr/lib/python2.7/dist-packages/numpy/f2py/src/fortranobject.h -> /tmp/tmpOUPHrs/src.linux-x86_64-2.7 adding '/tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_model-f2pywrappers2.f90' to sources. build_src: building npy-pkg config files running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize Gnu95FCompiler customize Gnu95FCompiler using build_ext building 'kmc_model' extension compiling C sources C 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
creating /tmp/tmpOUPHrs/tmp creating /tmp/tmpOUPHrs/tmp/tmpOUPHrs creating /tmp/tmpOUPHrs/tmp/tmpOUPHrs/src.linux-x86_64-2.7 compile 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' x86_64-linux-gnu-gcc: /tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_modelmodule.c In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1761:0, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:17, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from /tmp/tmpOUPHrs/src.linux-x86_64-2.7/fortranobject.h:13, from /tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_modelmodule.c:18: /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]
warning "Using deprecated NumPy API, disable it by " \
^ /tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_modelmodule.c: In function ‘f2py_setup_lattice’: /tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_modelmodule.c:4699:35: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types] f2py_lattice_def[i_f2py++].func = nr2lattice; ^ /tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_modelmodule.c:4700:35: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types] f2py_lattice_def[i_f2py++].func = lattice2nr; ^ /tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_modelmodule.c: In function ‘f2py_setup_proclist’: /tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_modelmodule.c:4747:36: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types] f2py_proclist_def[i_f2py++].func = seed_arr; ^ /tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_modelmodule.c: At top level: /tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_modelmodule.c:144:12: warning: ‘f2py_size’ defined but not used [-Wunused-function] static int f2py_size(PyArrayObject* var, ...) ^ x86_64-linux-gnu-gcc: /tmp/tmpOUPHrs/src.linux-x86_64-2.7/fortranobject.c In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1761:0, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:17, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from /tmp/tmpOUPHrs/src.linux-x86_64-2.7/fortranobject.h:13, from /tmp/tmpOUPHrs/src.linux-x86_64-2.7/fortranobject.c:2: /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]
warning "Using deprecated NumPy API, disable it by " \
^ compiling Fortran 90 module sources Fortran f77 compiler: /usr/bin/gfortran -Wall -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops Fortran f90 compiler: /usr/bin/gfortran -ffree-line-length-none -ffree-form -xf95-cpp-input -Wall -O3 -fimplicit-none -fPIC -O3 -funroll-loops Fortran 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 compile 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' extra options: '-J/tmp/tmpOUPHrs/ -I/tmp/tmpOUPHrs/' gfortran:f90: kind_values_f2py.f90 gfortran:f90: base.f90 gfortran:f90: lattice.f90 gfortran:f90: proclist.f90 compiling Fortran sources Fortran f77 compiler: /usr/bin/gfortran -Wall -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops Fortran f90 compiler: /usr/bin/gfortran -ffree-line-length-none -ffree-form -xf95-cpp-input -Wall -O3 -fimplicit-none -fPIC -O3 -funroll-loops Fortran 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 compile 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' extra options: '-J/tmp/tmpOUPHrs/ -I/tmp/tmpOUPHrs/' gfortran:f90: /tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_model-f2pywrappers2.f90 /tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_model-f2pywrappers2.f90:122:19:
Warning: Unused variable ‘j’ declared at (1) [-Wunused-variable] /tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_model-f2pywrappers2.f90:152:19:
Warning: Unused variable ‘j’ declared at (1) [-Wunused-variable] /tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_model-f2pywrappers2.f90:206:10:
Warning: Unused module variable ‘lattice2nr’ which has been explicitly imported at (1) [-Wunused-variable] /tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_model-f2pywrappers2.f90:206:10:
Warning: Unused module variable ‘nr2lattice’ which has been explicitly imported at (1) [-Wunused-variable] /tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_model-f2pywrappers2.f90:269:19:
Warning: Unused variable ‘j’ declared at (1) [-Wunused-variable] /tmp/tmpOUPHrs/src.linux-x86_64-2.7/kmc_model-f2pywrappers2.f90:295:10:
Warning: Unused module variable ‘seed_arr’ which has been explicitly imported at (1) [-Wunused-variable] /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 Removing build directory /tmp/tmpOUPHrs `