diff --git a/.gitignore b/.gitignore index 4379d05dd..79af9ef5e 100644 --- a/.gitignore +++ b/.gitignore @@ -42,6 +42,8 @@ test/**/last_conf.dat test/**/*log.dat test/**/trajectory.dat test/**/time.dat +test/OXPY/first_nucleotide.dat +test/OXPY/last_nucleotide.dat **/*pyc diff --git a/src/Backends/AnalysisBackend.h b/src/Backends/AnalysisBackend.h index 3cdf6f19b..ceeb8b774 100644 --- a/src/Backends/AnalysisBackend.h +++ b/src/Backends/AnalysisBackend.h @@ -52,8 +52,8 @@ class AnalysisBackend: public SimBackend { const FlattenedConfigInfo &flattened_conf(); - ConfigInfo *config_info() { - return _config_info; + std::shared_ptr config_info() { + return CONFIG_INFO; } llint get_conf_step() { diff --git a/test/OXPY/first_nucleotide_correct.dat b/test/OXPY/first_nucleotide_correct.dat new file mode 100644 index 000000000..1ad6b2028 --- /dev/null +++ b/test/OXPY/first_nucleotide_correct.dat @@ -0,0 +1,10 @@ +[-11.78911323 43.40048831 1.57645506] +[-14.14325234 40.56472505 2.0471197 ] +[-18.32734558 37.03027119 2.42922245] +[-23.77341355 35.3688551 1.82196622] +[-30.6031531 34.80713034 4.54497927] +[-34.02963687 36.94788357 9.20757146] +[-38.71207711 36.98956237 6.66388904] +[-37.41612362 38.95930485 5.18552101] +[-35.66393047 38.5800238 2.98663143] +[-38.16168017 34.77034427 5.37125748] diff --git a/test/OXPY/input_analysis b/test/OXPY/input_analysis new file mode 100644 index 000000000..8abc4850f --- /dev/null +++ b/test/OXPY/input_analysis @@ -0,0 +1,24 @@ +backend = CPU + +steps = 1e6 +newtonian_steps = 103 +diff_coeff = 2.50 +#pt = 0.1 +thermostat = john + +T = 20C +dt = 0.005 +verlet_skin = 0.05 + +topology = dsdna8.top +conf_file = non_existing_conf.dat +trajectory_file = trajectory_analysis.dat +refresh_vel = true +log_file = log.dat +no_stdout_energy = true +restart_step_counter = true +energy_file = energy.dat +print_conf_interval = 1e5 +print_energy_every = 1e3 +time_scale = linear +external_forces = false diff --git a/test/OXPY/oxpy_compare b/test/OXPY/oxpy_compare index f75e038d5..9044be12f 100644 --- a/test/OXPY/oxpy_compare +++ b/test/OXPY/oxpy_compare @@ -1 +1,2 @@ DiffFiles::last_nucleotide_correct.dat::last_nucleotide.dat +DiffFiles::first_nucleotide_correct.dat::first_nucleotide.dat diff --git a/test/OXPY/oxpy_input.py b/test/OXPY/oxpy_input.py index f41ec49e1..26a98bf02 100644 --- a/test/OXPY/oxpy_input.py +++ b/test/OXPY/oxpy_input.py @@ -26,4 +26,14 @@ def get_output_string(self, curr_step): # run 1k steps manager.run(1000) - \ No newline at end of file +with oxpy.Context(): + inp = oxpy.InputFile() + inp.init_from_filename("input_analysis") + # this object will make it possible to access the trajectory data + backend = oxpy.analysis.AnalysisBackend(inp) + + with open("first_nucleotide.dat", "w") as f: + # loop over all the configurations stored in the trajectory file + while backend.read_next_configuration(): + # print the position of the first nucleotide + print(backend.config_info().particles()[0].pos, file=f) diff --git a/test/OXPY/trajectory_analysis.dat b/test/OXPY/trajectory_analysis.dat new file mode 100644 index 000000000..585fa88b9 --- /dev/null +++ b/test/OXPY/trajectory_analysis.dat @@ -0,0 +1,190 @@ +t = 10000 +b = 20 20 20 +E = -1.2914906199289 -1.45279670375568 0.161306083826782 +-11.7891132290895 43.4004883137232 1.5764550555907 -0.991286424135234 -0.0657743306588943 0.114126958916581 0.00105389697137906 -0.870341957425904 -0.492446714320658 0.455052002639957 -0.335060089955537 0.214638721125006 -0.138201841736169 0.0022043178367733 0.134982567692249 +-11.7983076502892 42.8629282934969 1.58779546417067 -0.872727735750971 0.294687910729683 -0.389236861718869 -0.0692058309824777 -0.863901881734597 -0.498882843655143 -0.107650477369518 0.373296140172072 0.381553153637335 -0.562983136994975 0.285106723036868 -0.308316856612439 +-12.0585691042886 42.4187431400643 1.53181244721759 -0.249259790043162 0.509664102000315 -0.823475597816864 -0.109756673549918 -0.859702802284289 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