From 719836c6382d87999b70f6ca54393f55e7a7868f Mon Sep 17 00:00:00 2001 From: Lorenzo Rovigatti Date: Fri, 19 Aug 2022 09:31:56 +0200 Subject: [PATCH] Fix a bug related to the python bindings of the analysis backend Also add a test to catch these problems early --- .gitignore | 2 + src/Backends/AnalysisBackend.h | 4 +- test/OXPY/first_nucleotide_correct.dat | 10 ++ test/OXPY/input_analysis | 24 ++++ test/OXPY/oxpy_compare | 1 + test/OXPY/oxpy_input.py | 12 +- test/OXPY/trajectory_analysis.dat | 190 +++++++++++++++++++++++++ 7 files changed, 240 insertions(+), 3 deletions(-) create mode 100644 test/OXPY/first_nucleotide_correct.dat create mode 100644 test/OXPY/input_analysis create mode 100644 test/OXPY/trajectory_analysis.dat 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 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