diff --git a/meta_info_exploded/public.meta_dictionary/conserved_quantity.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/conserved_quantity.meta_info_entry.json
index 9fd868193a0316783a55f245fd58181a5d1ebcd2..208a9ad59f954b220007dce744716b6c231e301f 100644
--- a/meta_info_exploded/public.meta_dictionary/conserved_quantity.meta_info_entry.json
+++ b/meta_info_exploded/public.meta_dictionary/conserved_quantity.meta_info_entry.json
@@ -4,10 +4,8 @@
"meta_description":[
"The values of a quantity that should be conserved, along a sequence of frames ",
"(i.e., a trajectory). A frame is one section_single_configuration_calculation), ",
- "for example the total energy in the NVE ensemble. If not all frames have a ",
- "value the indices of the frames that have a value are stored in ",
- "frame_sequence_conserved_quantity_frames."],
- "meta_parent_section":"section_frame_sequence",
+ "for example the total energy in the NVE ensemble."],
+ "meta_parent_section":"section_single_configuration_calculation",
"meta_data_type":"float",
"meta_units":"J"
}
diff --git a/meta_info_exploded/public.meta_dictionary/frame_sequence_conserved_quantity.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/frame_sequence_conserved_quantity.meta_info_entry.json
deleted file mode 100644
index 6f249f672e176c628a1b1068d79d0611631cdcaa..0000000000000000000000000000000000000000
--- a/meta_info_exploded/public.meta_dictionary/frame_sequence_conserved_quantity.meta_info_entry.json
+++ /dev/null
@@ -1,17 +0,0 @@
-{
- "meta_name":"frame_sequence_conserved_quantity",
- "meta_type":"type-value",
- "meta_deprecated":true,
- "meta_description":[
- "(deprecated) Array containing the values of a quantity that should be ",
- "conserved, along a sequence of frames (i.e., a trajectory). A frame is one ",
- "section_single_configuration_calculation), for example the total energy in the ",
- "NVE ensemble. If not all frames have a value the indices of the frames that ",
- "have a value are stored in frame_sequence_conserved_quantity_frames."],
- "meta_parent_section":"section_frame_sequence",
- "meta_data_type":"float",
- "meta_dimension":[{
- "meta_dimension_symbolic":"number_of_conserved_quantity_evaluations_in_sequence"
- }],
- "meta_units":"J"
-}
diff --git a/meta_info_exploded/public.meta_dictionary/frame_sequence_conserved_quantity_frames.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/frame_sequence_conserved_quantity_frames.meta_info_entry.json
deleted file mode 100644
index 397a5c90fda2db986a71b33f5491081a9f282ee6..0000000000000000000000000000000000000000
--- a/meta_info_exploded/public.meta_dictionary/frame_sequence_conserved_quantity_frames.meta_info_entry.json
+++ /dev/null
@@ -1,15 +0,0 @@
-{
- "meta_name":"frame_sequence_conserved_quantity_frames",
- "meta_type":"type-value",
- "meta_description":[
- "Array containing the strictly increasing indices of the frames the ",
- "frame_sequence_conserved_quantity values refers to. If not given it defaults to ",
- "the trivial mapping 0,1,..."],
- "meta_parent_section":"section_frame_sequence",
- "meta_abstract_types":[
- "derived_quantity"],
- "meta_data_type":"int",
- "meta_dimension":[{
- "meta_dimension_symbolic":"number_of_conserved_quantity_evaluations_in_sequence"
- }]
-}
diff --git a/meta_info_exploded/public.meta_dictionary/frame_sequence_conserved_quantity_stats.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/frame_sequence_conserved_quantity_stats.meta_info_entry.json
index 8219dae408d6ffc4dc83e82d62c38dca2757373d..d90fd61e3d0ce7fa4c6d18794ae8a0d7e1c00780 100644
--- a/meta_info_exploded/public.meta_dictionary/frame_sequence_conserved_quantity_stats.meta_info_entry.json
+++ b/meta_info_exploded/public.meta_dictionary/frame_sequence_conserved_quantity_stats.meta_info_entry.json
@@ -2,15 +2,14 @@
"meta_name":"frame_sequence_conserved_quantity_stats",
"meta_type":"type-value",
"meta_description":[
- "Average value of energy-like frame_sequence_conserved_quantity, and its ",
- "standard deviation, over this sequence of frames (i.e., a trajectory, a frame ",
- "is one section_single_configuration_calculation)."],
+ "Average value of energy-like conserved_quantity, its ",
+ "standard deviation, and number of samples over this sequence of frames."],
"meta_parent_section":"section_frame_sequence",
"meta_abstract_types":[
"derived_quantity"],
"meta_data_type":"float",
"meta_dimension":[{
- "meta_dimension_fixed":2
+ "meta_dimension_fixed":3
}],
"meta_units":"J"
}
diff --git a/meta_info_exploded/public.meta_dictionary/frame_sequence_kinetic_energy.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/frame_sequence_kinetic_energy.meta_info_entry.json
deleted file mode 100644
index 298a3422b748ad3239de4930a41d210c9e89ed43..0000000000000000000000000000000000000000
--- a/meta_info_exploded/public.meta_dictionary/frame_sequence_kinetic_energy.meta_info_entry.json
+++ /dev/null
@@ -1,16 +0,0 @@
-{
- "meta_name":"frame_sequence_kinetic_energy",
- "meta_type":"type-value",
- "meta_description":[
- "(deprecated) Array containing the values of the kinetic energy along this ",
- "sequence of frames (i.e., a trajectory, a frame is one ",
- "section_single_configuration_calculation). If not all frames have a value the ",
- "indices of the frames that have a value are stored in ",
- "frame_sequence_kinetic_energy_frames."],
- "meta_parent_section":"section_frame_sequence",
- "meta_data_type":"float",
- "meta_dimension":[{
- "meta_dimension_symbolic":"number_of_kinetic_energies_in_sequence"
- }],
- "meta_units":"J"
-}
diff --git a/meta_info_exploded/public.meta_dictionary/frame_sequence_kinetic_energy_frames.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/frame_sequence_kinetic_energy_frames.meta_info_entry.json
deleted file mode 100644
index 6ca0ad6b0b5cbd656ce292c253bd9f2d67ca0d05..0000000000000000000000000000000000000000
--- a/meta_info_exploded/public.meta_dictionary/frame_sequence_kinetic_energy_frames.meta_info_entry.json
+++ /dev/null
@@ -1,15 +0,0 @@
-{
- "meta_name":"frame_sequence_kinetic_energy_frames",
- "meta_type":"type-value",
- "meta_description":[
- "Array containing the strictly increasing indices referring to the frames of ",
- "frame_sequence_kinetic_energy. If not given it defaults to the trivial mapping ",
- "0,1,..."],
- "meta_parent_section":"section_frame_sequence",
- "meta_abstract_types":[
- "derived_quantity"],
- "meta_data_type":"int",
- "meta_dimension":[{
- "meta_dimension_symbolic":"number_of_kinetic_energies_in_sequence"
- }]
-}
diff --git a/meta_info_exploded/public.meta_dictionary/frame_sequence_kinetic_energy_stats.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/frame_sequence_kinetic_energy_stats.meta_info_entry.json
index 1218a827d09740e17a5f05de27e55a4edb71e44a..d533a8b9429a3f8b2c2573aebc93aeefdb160dea 100644
--- a/meta_info_exploded/public.meta_dictionary/frame_sequence_kinetic_energy_stats.meta_info_entry.json
+++ b/meta_info_exploded/public.meta_dictionary/frame_sequence_kinetic_energy_stats.meta_info_entry.json
@@ -2,14 +2,13 @@
"meta_name":"frame_sequence_kinetic_energy_stats",
"meta_type":"type-value",
"meta_description":[
- "Average kinetic energy and its standard deviation over this sequence of frames ",
- "(i.e., a trajectory, a frame is one section_single_configuration_calculation)."],
+ "Average kinetic energy, its standard deviation and number of samples over this sequence of frames."],
"meta_parent_section":"section_frame_sequence",
"meta_abstract_types":[
"derived_quantity"],
"meta_data_type":"float",
"meta_dimension":[{
- "meta_dimension_fixed":2
+ "meta_dimension_fixed":3
}],
"meta_units":"J"
}
diff --git a/meta_info_exploded/public.meta_dictionary/frame_sequence_local_frames_ref.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/frame_sequence_local_frames_ref.meta_info_entry.json
deleted file mode 100644
index 0e0a0dbfab6f28df19cf2c542dbc4022c0619023..0000000000000000000000000000000000000000
--- a/meta_info_exploded/public.meta_dictionary/frame_sequence_local_frames_ref.meta_info_entry.json
+++ /dev/null
@@ -1,19 +0,0 @@
-{
- "meta_name":"frame_sequence_local_frames_ref",
- "meta_type":"type-value",
- "meta_description":[
- "(deprecated) Reference from each frame (a frame is one ",
- "section_single_configuration_calculation) in this section_frame_sequence to the ",
- "corresponding section_single_configuration_calculation. Each ",
- "section_frame_sequence binds a collection of ",
- "section_single_configuration_calculation, because they all belong to, e.g., a ",
- "molecular dynamics trajectory, or geometry optimization. The full information ",
- "for each frame is stored in section_single_configuration_calculation and this ",
- "metadata establishes the link for each frame."],
- "meta_parent_section":"section_frame_sequence",
- "meta_data_type":"reference",
- "meta_dimension":[{
- "meta_dimension_symbolic":"number_of_frames_in_sequence"
- }],
- "meta_referenced_section":"section_single_configuration_calculation"
-}
diff --git a/meta_info_exploded/public.meta_dictionary/frame_sequence_potential_energy.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/frame_sequence_potential_energy.meta_info_entry.json
deleted file mode 100644
index e4430360ec3f22cfe188f64a8285027be9490db2..0000000000000000000000000000000000000000
--- a/meta_info_exploded/public.meta_dictionary/frame_sequence_potential_energy.meta_info_entry.json
+++ /dev/null
@@ -1,18 +0,0 @@
-{
- "meta_name":"frame_sequence_potential_energy",
- "meta_type":"type-value",
- "meta_description":[
- "(deprecated) Array containing the value of the potential energy along this ",
- "sequence of frames (i.e., a trajectory, a frame is one ",
- "section_single_configuration_calculation). This is equal to energy_total of the ",
- "corresponding section_single_configuration_calculation and repeated here in a ",
- "summary array for easier access. If not all frames have a value the indices of ",
- "the frames that have a value are stored in ",
- "frame_sequence_potential_energy_frames."],
- "meta_parent_section":"section_frame_sequence",
- "meta_data_type":"float",
- "meta_dimension":[{
- "meta_dimension_symbolic":"number_of_potential_energies_in_sequence"
- }],
- "meta_units":"J"
-}
diff --git a/meta_info_exploded/public.meta_dictionary/frame_sequence_potential_energy_frames.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/frame_sequence_potential_energy_frames.meta_info_entry.json
deleted file mode 100644
index 84c58ff9a8f0a9da8136db09888d2e8304dfd37a..0000000000000000000000000000000000000000
--- a/meta_info_exploded/public.meta_dictionary/frame_sequence_potential_energy_frames.meta_info_entry.json
+++ /dev/null
@@ -1,15 +0,0 @@
-{
- "meta_name":"frame_sequence_potential_energy_frames",
- "meta_type":"type-value",
- "meta_description":[
- "Array containing the strictly increasing indices referring to the frames of ",
- "frame_sequence_potential_energy. If not given it defaults to the trivial ",
- "mapping 0,1,..."],
- "meta_parent_section":"section_frame_sequence",
- "meta_abstract_types":[
- "derived_quantity"],
- "meta_data_type":"int",
- "meta_dimension":[{
- "meta_dimension_symbolic":"number_of_potential_energies_in_sequence"
- }]
-}
diff --git a/meta_info_exploded/public.meta_dictionary/frame_sequence_potential_energy_stats.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/frame_sequence_potential_energy_stats.meta_info_entry.json
index 1a37baff1c7203466d75ddabd4755527ad51dc43..46b6dde31c8a62e483886d4a8ba0d998cb89469a 100644
--- a/meta_info_exploded/public.meta_dictionary/frame_sequence_potential_energy_stats.meta_info_entry.json
+++ b/meta_info_exploded/public.meta_dictionary/frame_sequence_potential_energy_stats.meta_info_entry.json
@@ -2,15 +2,14 @@
"meta_name":"frame_sequence_potential_energy_stats",
"meta_type":"type-value",
"meta_description":[
- "Average potential energy and its standard deviation over this sequence of ",
- "frames (i.e., a trajectory, a frame is one ",
- "section_single_configuration_calculation)."],
+ "Average potential energy, its standard deviation and number of samples over this sequence of ",
+ "frames."],
"meta_parent_section":"section_frame_sequence",
"meta_abstract_types":[
"derived_quantity"],
"meta_data_type":"float",
"meta_dimension":[{
- "meta_dimension_fixed":2
+ "meta_dimension_fixed":3
}],
"meta_units":"J"
}
diff --git a/meta_info_exploded/public.meta_dictionary/frame_sequence_pressure.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/frame_sequence_pressure.meta_info_entry.json
deleted file mode 100644
index fd37c447d74e1f28d8ee6ec3ecf2edc3d9e115bb..0000000000000000000000000000000000000000
--- a/meta_info_exploded/public.meta_dictionary/frame_sequence_pressure.meta_info_entry.json
+++ /dev/null
@@ -1,16 +0,0 @@
-{
- "meta_name":"frame_sequence_pressure",
- "meta_type":"type-value",
- "meta_description":[
- "(deprecated) Array containing the values of the pressure (one third of the ",
- "trace of the stress tensor) along this sequence of frames (a frame is one ",
- "section_single_configuration_calculation). If not all frames have a value the ",
- "indices of the frames that have a value are stored in ",
- "frame_sequence_pressure_frames."],
- "meta_parent_section":"section_frame_sequence",
- "meta_data_type":"float",
- "meta_dimension":[{
- "meta_dimension_symbolic":"number_of_pressure_evaluations_in_sequence"
- }],
- "meta_units":"Pa"
-}
diff --git a/meta_info_exploded/public.meta_dictionary/frame_sequence_pressure_frames.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/frame_sequence_pressure_frames.meta_info_entry.json
deleted file mode 100644
index 8a2871af7fb41385939924008b16f09aeb2614af..0000000000000000000000000000000000000000
--- a/meta_info_exploded/public.meta_dictionary/frame_sequence_pressure_frames.meta_info_entry.json
+++ /dev/null
@@ -1,15 +0,0 @@
-{
- "meta_name":"frame_sequence_pressure_frames",
- "meta_type":"type-value",
- "meta_description":[
- "Array containing the strictly increasing indices referring to the frames of ",
- "frame_sequence_pressure. If not given it defaults to the trivial mapping ",
- "0,1,..."],
- "meta_parent_section":"section_frame_sequence",
- "meta_abstract_types":[
- "derived_quantity"],
- "meta_data_type":"int",
- "meta_dimension":[{
- "meta_dimension_symbolic":"number_of_pressure_evaluations_in_sequence"
- }]
-}
diff --git a/meta_info_exploded/public.meta_dictionary/frame_sequence_pressure_stats.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/frame_sequence_pressure_stats.meta_info_entry.json
index 838236d376b7f9b20ee2dcdf5f4db2d1ef707ff8..9568bfa6bb59928c6470bdd0f1a193d40a4f7dd5 100644
--- a/meta_info_exploded/public.meta_dictionary/frame_sequence_pressure_stats.meta_info_entry.json
+++ b/meta_info_exploded/public.meta_dictionary/frame_sequence_pressure_stats.meta_info_entry.json
@@ -2,15 +2,15 @@
"meta_name":"frame_sequence_pressure_stats",
"meta_type":"type-value",
"meta_description":[
- "Average pressure (one third of the trace of the stress tensor) and standard ",
- "deviation over this sequence of frames (i.e., a trajectory, a frame is one ",
+ "Average pressure (one third of the trace of the stress tensor), standard ",
+ "deviation and number of samples over this sequence of frames (i.e., a trajectory, a frame is one ",
"section_single_configuration_calculation)."],
"meta_parent_section":"section_frame_sequence",
"meta_abstract_types":[
"derived_quantity"],
"meta_data_type":"float",
"meta_dimension":[{
- "meta_dimension_fixed":2
+ "meta_dimension_fixed":3
}],
"meta_units":"Pa"
}
diff --git a/meta_info_exploded/public.meta_dictionary/frame_sequence_temperature.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/frame_sequence_temperature.meta_info_entry.json
deleted file mode 100644
index 2c6cb20a31c54eae74a3a165bacee0e95a2c9773..0000000000000000000000000000000000000000
--- a/meta_info_exploded/public.meta_dictionary/frame_sequence_temperature.meta_info_entry.json
+++ /dev/null
@@ -1,17 +0,0 @@
-{
- "meta_name":"frame_sequence_temperature",
- "meta_type":"type-value",
- "meta_description":[
- "(deprecated) Array containing the values of the instantaneous temperature (a ",
- "quantity, proportional to frame_sequence_kinetic_energy, whose ensemble average ",
- "equals the thermodynamic temperature) along this sequence of frames (i.e., a ",
- "trajectory, a frame is one section_single_configuration_calculation). If not ",
- "all frames have a value the indices of the frames that have a value are stored ",
- "in frame_sequence_temperature_frames."],
- "meta_parent_section":"section_frame_sequence",
- "meta_data_type":"float",
- "meta_dimension":[{
- "meta_dimension_symbolic":"number_of_temperatures_in_sequence"
- }],
- "meta_units":"K"
-}
diff --git a/meta_info_exploded/public.meta_dictionary/frame_sequence_temperature_frames.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/frame_sequence_temperature_frames.meta_info_entry.json
deleted file mode 100644
index 7db00a014115cf29ce6de2d9346e4db8ff70090e..0000000000000000000000000000000000000000
--- a/meta_info_exploded/public.meta_dictionary/frame_sequence_temperature_frames.meta_info_entry.json
+++ /dev/null
@@ -1,15 +0,0 @@
-{
- "meta_name":"frame_sequence_temperature_frames",
- "meta_type":"type-value",
- "meta_description":[
- "Array containing the strictly increasing indices referring to the frames of ",
- "frame_sequence_temperature. If not given it defaults to the trivial mapping ",
- "0,1,..."],
- "meta_parent_section":"section_frame_sequence",
- "meta_abstract_types":[
- "derived_quantity"],
- "meta_data_type":"int",
- "meta_dimension":[{
- "meta_dimension_symbolic":"number_of_temperatures_in_sequence"
- }]
-}
diff --git a/meta_info_exploded/public.meta_dictionary/frame_sequence_temperature_stats.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/frame_sequence_temperature_stats.meta_info_entry.json
index ead845733b51ce3e5bb6be8564ba185a364b8e22..37359fdc51444b1c1b6955343e1422c8a80781cc 100644
--- a/meta_info_exploded/public.meta_dictionary/frame_sequence_temperature_stats.meta_info_entry.json
+++ b/meta_info_exploded/public.meta_dictionary/frame_sequence_temperature_stats.meta_info_entry.json
@@ -2,14 +2,13 @@
"meta_name":"frame_sequence_temperature_stats",
"meta_type":"type-value",
"meta_description":[
- "Average temperature and its standard deviation over this sequence of frames ",
- "(i.e., a trajectory, a frame is one section_single_configuration_calculation)."],
+ "Average temperature, its standard deviation and number for samples over this sequence of frames ."],
"meta_parent_section":"section_frame_sequence",
"meta_abstract_types":[
"derived_quantity"],
"meta_data_type":"float",
"meta_dimension":[{
- "meta_dimension_fixed":2
+ "meta_dimension_fixed":3
}],
"meta_units":"K"
}
diff --git a/meta_info_exploded/public.meta_dictionary/frame_sequence_to_sampling_ref.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/frame_sequence_to_sampling_ref.meta_info_entry.json
deleted file mode 100644
index f7602d81beaa2922b23e0fb535b0c3df58400d4f..0000000000000000000000000000000000000000
--- a/meta_info_exploded/public.meta_dictionary/frame_sequence_to_sampling_ref.meta_info_entry.json
+++ /dev/null
@@ -1,12 +0,0 @@
-{
- "meta_name":"frame_sequence_to_sampling_ref",
- "meta_type":"type-value",
- "meta_description":[
- "(deprecated) Reference from the present section_frame_sequence to the ",
- "section_sampling_method, that defines the parameters used in this sequence of ",
- "frames (i.e., a trajectory, a frame is one ",
- "section_single_configuration_calculation)."],
- "meta_parent_section":"section_frame_sequence",
- "meta_data_type":"reference",
- "meta_referenced_section":"section_sampling_method"
-}
diff --git a/meta_info_exploded/public.meta_dictionary/frame_sequence_user_quantity.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/frame_sequence_user_quantity.meta_info_entry.json
deleted file mode 100644
index a74a1799bb07e910c9f5d7237f9016e6c4899ef9..0000000000000000000000000000000000000000
--- a/meta_info_exploded/public.meta_dictionary/frame_sequence_user_quantity.meta_info_entry.json
+++ /dev/null
@@ -1,19 +0,0 @@
-{
- "meta_name":"frame_sequence_user_quantity",
- "meta_type":"type-value",
- "meta_description":[
- "(deprecated) Array containing the values of the user-defined quantity defined ",
- "in frame_sequence_user_quantity_name, evaluated along this sequence of frames ",
- "(i.e., trajectory, a frame is one section_single_configuration_calculation). If ",
- "not all frames have a value the indices of the frames that have a value are ",
- "stored in frame_sequence_kinetic_energy_frames. If not all frames have a value ",
- "the indices of the frames that have a value are stored in ",
- "frame_sequence_kinetic_energy_frames."],
- "meta_parent_section":"section_frame_sequence_user_quantity",
- "meta_data_type":"float",
- "meta_dimension":[{
- "meta_dimension_symbolic":"number_of_frame_sequence_user_quantity_evaluations_in_sequence"
- },{
- "meta_dimension_symbolic":"number_of_frame_sequence_user_quantity_components"
- }]
-}
diff --git a/meta_info_exploded/public.meta_dictionary/frame_sequence_user_quantity_frames.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/frame_sequence_user_quantity_frames.meta_info_entry.json
deleted file mode 100644
index aa867cf039abeb70869d672bae8c927ec10105b5..0000000000000000000000000000000000000000
--- a/meta_info_exploded/public.meta_dictionary/frame_sequence_user_quantity_frames.meta_info_entry.json
+++ /dev/null
@@ -1,13 +0,0 @@
-{
- "meta_name":"frame_sequence_user_quantity_frames",
- "meta_type":"type-value",
- "meta_description":[
- "(deprecated) Array containing the strictly increasing indices referring to the ",
- "frames of frame_sequence_user_quantity. If not given it defaults to the trivial ",
- "mapping 0,1,..."],
- "meta_parent_section":"section_frame_sequence_user_quantity",
- "meta_data_type":"int",
- "meta_dimension":[{
- "meta_dimension_symbolic":"number_of_frame_sequence_user_quantity_evaluations_in_sequence"
- }]
-}
diff --git a/meta_info_exploded/public.meta_dictionary/frame_sequence_user_quantity_name.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/frame_sequence_user_quantity_name.meta_info_entry.json
deleted file mode 100644
index 21232443f6f63d195437c8dfc15205309f990c99..0000000000000000000000000000000000000000
--- a/meta_info_exploded/public.meta_dictionary/frame_sequence_user_quantity_name.meta_info_entry.json
+++ /dev/null
@@ -1,16 +0,0 @@
-{
- "meta_name":"frame_sequence_user_quantity_name",
- "meta_type":"type-value",
- "meta_description":[
- "(deprecated) Descriptive name of a user-defined quantity, sampled along this ",
- "sequence of frames (i.e., a trajectory, a frame is one ",
- "section_single_configuration_calculation). Dedicated metadata are created for ",
- "the conserved energy-like quantity (frame_sequence_conserved_quantity), the ",
- "kinetic and potential energies (frame_sequence_kinetic_energy and ",
- "frame_sequence_potential_energy), the instantaneous temperature ",
- "(frame_sequence_temperature) and pressure (frame_sequence_pressure). This ",
- "metadata should be used for other quantities that are monitored along a ",
- "sequence of frames."],
- "meta_parent_section":"section_frame_sequence_user_quantity",
- "meta_data_type":"string"
-}
diff --git a/meta_info_exploded/public.meta_dictionary/frame_sequence_user_quantity_stats.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/frame_sequence_user_quantity_stats.meta_info_entry.json
deleted file mode 100644
index 85c6906adfe9cc392d8ede2c8e9768c24f69f0e8..0000000000000000000000000000000000000000
--- a/meta_info_exploded/public.meta_dictionary/frame_sequence_user_quantity_stats.meta_info_entry.json
+++ /dev/null
@@ -1,15 +0,0 @@
-{
- "meta_name":"frame_sequence_user_quantity_stats",
- "meta_type":"type-value",
- "meta_description":[
- "(deprecated) Average of frame_sequence_user_quantity and its standard deviation ",
- "in this sequence of frames (i.e., a trajectory, a frame is one ",
- "section_single_configuration_calculation)."],
- "meta_parent_section":"section_frame_sequence_user_quantity",
- "meta_data_type":"float",
- "meta_dimension":[{
- "meta_dimension_fixed":2
- },{
- "meta_dimension_symbolic":"number_of_frame_sequence_user_quantity_components"
- }]
-}
diff --git a/meta_info_exploded/public.meta_dictionary/number_of_frame_sequence_user_quantity_components.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/number_of_frame_sequence_user_quantity_components.meta_info_entry.json
deleted file mode 100644
index 87df668b83d2622641e85527cd7022e80c593e61..0000000000000000000000000000000000000000
--- a/meta_info_exploded/public.meta_dictionary/number_of_frame_sequence_user_quantity_components.meta_info_entry.json
+++ /dev/null
@@ -1,18 +0,0 @@
-{
- "meta_name":"number_of_frame_sequence_user_quantity_components",
- "meta_type":"type-dimension",
- "meta_description":[
- "(deprecated) Gives the number of user-defined quantity defined by ",
- "frame_sequence_user_quantity_name and monitored in a sequence of frames. A ",
- "sequence is a trajectory, which can have number_of_frames_in_sequence each ",
- "representing one section_single_configuration_calculation section.\n",
- "\n",
- "Dedicated metadata monitored along a sequence of frames are created for the ",
- "conserved energy-like quantity (frame_sequence_conserved_quantity), the kinetic ",
- "and potential energies ([frame_sequence_kinetic_energy and ",
- "frame_sequence_potential_energy](frame_sequence_kinetic_energy and ",
- "frame_sequence_potential_energy)), the instantaneous temperature ",
- "(frame_sequence_temperature) and the pressure ",
- "(frame_sequence_pressure)."],
- "meta_parent_section":"section_frame_sequence_user_quantity"
-}
diff --git a/meta_info_exploded/public.meta_dictionary/number_of_frame_sequence_user_quantity_evaluations_in_sequence.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/number_of_frame_sequence_user_quantity_evaluations_in_sequence.meta_info_entry.json
deleted file mode 100644
index c2f5e7cc855da4392df1889205641a1366c5f7d8..0000000000000000000000000000000000000000
--- a/meta_info_exploded/public.meta_dictionary/number_of_frame_sequence_user_quantity_evaluations_in_sequence.meta_info_entry.json
+++ /dev/null
@@ -1,11 +0,0 @@
-{
- "meta_name":"number_of_frame_sequence_user_quantity_evaluations_in_sequence",
- "meta_type":"type-dimension",
- "meta_description":[
- "(deprecated) Gives the number of user defined quantity evaluations along a ",
- "sequence of frame_sequence_user_quantity frames. A sequence is a trajectory, ",
- "which can have number_of_frames_in_sequence each representing one ",
- "section_single_configuration_calculation ",
- "section."],
- "meta_parent_section":"section_frame_sequence_user_quantity"
-}
diff --git a/meta_info_exploded/public.meta_dictionary/number_of_user_quantity_components.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/number_of_user_quantity_components.meta_info_entry.json
index 6dcbd2d82afdda5ab66d9e1018fa1c58316ca7e0..21b4a9f860dfccdf4de6df05dbcf0377411f6107 100644
--- a/meta_info_exploded/public.meta_dictionary/number_of_user_quantity_components.meta_info_entry.json
+++ b/meta_info_exploded/public.meta_dictionary/number_of_user_quantity_components.meta_info_entry.json
@@ -2,17 +2,7 @@
"meta_name":"number_of_user_quantity_components",
"meta_type":"type-dimension",
"meta_description":[
- "Gives the number of user-defined quantity defined by ",
- "frame_sequence_user_quantity_name and monitored in a sequence of frames. A ",
- "sequence is a trajectory, which can have number_of_frames_in_sequence each ",
- "representing one section_single_configuration_calculation section.\n",
- "\n",
- "Dedicated metadata monitored along a sequence of frames are created for the ",
- "conserved energy-like quantity (frame_sequence_conserved_quantity), the kinetic ",
- "and potential energies ([frame_sequence_kinetic_energy and ",
- "frame_sequence_potential_energy](frame_sequence_kinetic_energy and ",
- "frame_sequence_potential_energy)), the instantaneous temperature ",
- "(frame_sequence_temperature) and the pressure ",
- "(frame_sequence_pressure)."],
- "meta_parent_section":"section_user_quantity_definition"
+ "Gives the number of components of user-defined quantity stored in user_defined_quantity. It should be the value defined in ",
+ "user_quantity_components of user_quantity_definition_ref."],
+ "meta_parent_section":"section_user_quantity"
}
diff --git a/meta_info_exploded/public.meta_dictionary/number_of_user_quantity_stats_components.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/number_of_user_quantity_stats_components.meta_info_entry.json
new file mode 100644
index 0000000000000000000000000000000000000000..4b9bd12ebef7d035be8c593de5c2c1641bb3d6f9
--- /dev/null
+++ b/meta_info_exploded/public.meta_dictionary/number_of_user_quantity_stats_components.meta_info_entry.json
@@ -0,0 +1,8 @@
+{
+ "meta_name":"number_of_user_quantity_stats_components",
+ "meta_type":"type-dimension",
+ "meta_description":[
+ "Gives the number of components of user-defined quantity stored in user_defined_quantity. It should be the value defined in ",
+ "user_quantity_components of user_quantity_stats_to_user_quantity_definition_ref."],
+ "meta_parent_section":"section_user_quantity_stats"
+}
diff --git a/meta_info_exploded/public.meta_dictionary/section_frame_sequence_user_quantity.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/section_frame_sequence_user_quantity.meta_info_entry.json
deleted file mode 100644
index 96801ba168ed634046bcb3a756b6b880abe9874b..0000000000000000000000000000000000000000
--- a/meta_info_exploded/public.meta_dictionary/section_frame_sequence_user_quantity.meta_info_entry.json
+++ /dev/null
@@ -1,10 +0,0 @@
-{
- "meta_name":"section_frame_sequence_user_quantity",
- "meta_type":"type-section",
- "meta_description":[
- "(deprecated) Section collecting some user-defined quantities evaluated along a ",
- "sequence of frame."],
- "meta_parent_section":"section_frame_sequence",
- "meta_repeats":true,
- "meta_context_identifier":[]
-}
diff --git a/meta_info_exploded/public.meta_dictionary/section_user_quantity_definition.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/section_user_quantity_definition.meta_info_entry.json
index de8fea0a946876f3718b774106e535b6bc4c90f2..e08976d776a54f9f21b07d6d2965a9e2984985dd 100644
--- a/meta_info_exploded/public.meta_dictionary/section_user_quantity_definition.meta_info_entry.json
+++ b/meta_info_exploded/public.meta_dictionary/section_user_quantity_definition.meta_info_entry.json
@@ -4,7 +4,7 @@
"meta_description":[
"Section collecting some user-defined quantities evaluated along a sequence of ",
"frame."],
- "meta_parent_section":"section_frame_sequence",
+ "meta_parent_section":"section_run",
"meta_repeats":true,
"meta_context_identifier":[]
}
diff --git a/meta_info_exploded/public.meta_dictionary/section_user_quantity_stats.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/section_user_quantity_stats.meta_info_entry.json
new file mode 100644
index 0000000000000000000000000000000000000000..206382538b087fa548f86dabc63285d71ee40bed
--- /dev/null
+++ b/meta_info_exploded/public.meta_dictionary/section_user_quantity_stats.meta_info_entry.json
@@ -0,0 +1,11 @@
+{
+ "meta_name":"section_user_quantity_stats",
+ "meta_type":"type-section",
+ "meta_description":[
+ "Section collecting the stats of the user-defined quantity ",
+ "user_quantity_stats_to_user_quantity_definition_ref evaluated along this ",
+ "sequence of frames."],
+ "meta_parent_section":"section_frame_sequence",
+ "meta_repeats":true,
+ "meta_context_identifier":[]
+}
diff --git a/meta_info_exploded/public.meta_dictionary/single_configuration_to_calculation_method_ref.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/single_configuration_to_calculation_method_ref.meta_info_entry.json
deleted file mode 100644
index 5b6b098fd01fe48f7ceb07b5f8209ef7eb8ba861..0000000000000000000000000000000000000000
--- a/meta_info_exploded/public.meta_dictionary/single_configuration_to_calculation_method_ref.meta_info_entry.json
+++ /dev/null
@@ -1,10 +0,0 @@
-{
- "meta_name":"single_configuration_to_calculation_method_ref",
- "meta_type":"type-value",
- "meta_description":[
- "(deprecated) Reference to the method used for the calculation in ",
- "section_single_configuration_calculation."],
- "meta_parent_section":"section_single_configuration_calculation",
- "meta_data_type":"reference",
- "meta_referenced_section":"section_method"
-}
diff --git a/meta_info_exploded/public.meta_dictionary/user_quantity_components.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/user_quantity_components.meta_info_entry.json
new file mode 100644
index 0000000000000000000000000000000000000000..7b52f997bf04415898a066fda65eb60b23e06755
--- /dev/null
+++ b/meta_info_exploded/public.meta_dictionary/user_quantity_components.meta_info_entry.json
@@ -0,0 +1,12 @@
+{
+ "meta_name":"user_quantity_components",
+ "meta_type":"type-value",
+ "meta_description":[
+ "Gives the number of components of the user-defined quantity defined by ",
+ "user_quantity_name and stored in the monitored in a sequence of frames. A ",
+ "sequence is a trajectory, which can have number_of_frames_in_sequence each ",
+ "representing one section_single_configuration_calculation section.\n"],
+ "meta_data_type": "int"
+ "meta_default_value": 1
+ "meta_parent_section":"section_user_quantity_definition"
+}
diff --git a/meta_info_exploded/public.meta_dictionary/user_quantity_frames.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/user_quantity_frames.meta_info_entry.json
deleted file mode 100644
index 0aa3cd8e035812297fd09473ab5fbd26e5178fee..0000000000000000000000000000000000000000
--- a/meta_info_exploded/public.meta_dictionary/user_quantity_frames.meta_info_entry.json
+++ /dev/null
@@ -1,15 +0,0 @@
-{
- "meta_name":"user_quantity_frames",
- "meta_type":"type-value",
- "meta_description":[
- "Array containing the strictly increasing indices referring to the frames of ",
- "frame_sequence_user_quantity. If not given it defaults to the trivial mapping ",
- "0,1,..."],
- "meta_parent_section":"section_user_quantity_definition",
- "meta_abstract_types":[
- "derived_quantity"],
- "meta_data_type":"int",
- "meta_dimension":[{
- "meta_dimension_symbolic":"number_of_user_quantity_evaluations_in_sequence"
- }]
-}
diff --git a/meta_info_exploded/public.meta_dictionary/user_quantity_stats.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/user_quantity_stats.meta_info_entry.json
index 570f5a03e1d0ac1e52e36d651ae6386e3fecf6ec..11e1f8f9f4f23e060658d20010649b34f809ba9f 100644
--- a/meta_info_exploded/public.meta_dictionary/user_quantity_stats.meta_info_entry.json
+++ b/meta_info_exploded/public.meta_dictionary/user_quantity_stats.meta_info_entry.json
@@ -2,16 +2,15 @@
"meta_name":"user_quantity_stats",
"meta_type":"type-value",
"meta_description":[
- "Average of frame_sequence_user_quantity and its standard deviation in this ",
- "sequence of frames (i.e., a trajectory, a frame is one ",
- "section_single_configuration_calculation)."],
- "meta_parent_section":"section_user_quantity_definition",
+ "Average of frame_sequence_user_quantity, its standard deviation and the number of samples in the",
+ "section_frame_sequence."],
+ "meta_parent_section":"section_user_quantity_stats",
"meta_abstract_types":[
"derived_quantity"],
"meta_data_type":"float",
"meta_dimension":[{
- "meta_dimension_fixed":2
+ "meta_dimension_fixed":3
},{
- "meta_dimension_symbolic":"number_of_user_quantity_components"
+ "meta_dimension_symbolic":"number_of_user_quantity_stats_components"
}]
}
diff --git a/meta_info_exploded/public.meta_dictionary/user_quantity_stats_to_user_quantity_definition_ref.meta_info_entry.json b/meta_info_exploded/public.meta_dictionary/user_quantity_stats_to_user_quantity_definition_ref.meta_info_entry.json
new file mode 100644
index 0000000000000000000000000000000000000000..6e469dcf6a48619598e78b33b6574891db6b0eea
--- /dev/null
+++ b/meta_info_exploded/public.meta_dictionary/user_quantity_stats_to_user_quantity_definition_ref.meta_info_entry.json
@@ -0,0 +1,10 @@
+{
+ "meta_name":"user_quantity_stats_to_user_quantity_definition_ref",
+ "meta_type":"type-value",
+ "meta_description":[
+ "Reference the user_quantity_definition the user_quantity_stats refer ",
+ "to."],
+ "meta_parent_section":"section_user_quantity_stats",
+ "meta_data_type":"reference",
+ "meta_referenced_section":"section_user_quantity_definition"
+}
diff --git a/renames/fplo_input_autogenerated.renames b/renames/fplo.renames
similarity index 100%
rename from renames/fplo_input_autogenerated.renames
rename to renames/fplo.renames
diff --git a/renames/octopus_autogenerated.renames b/renames/octopus.renames
similarity index 100%
rename from renames/octopus_autogenerated.renames
rename to renames/octopus.renames
diff --git a/renames/renamer.py b/renames/renamer.py
index 0c04960dd74896329f95d973db59dada6454c7aa..6ec344b35b98090bb9a0b23e4b76f4c2b2d51fa0 100644
--- a/renames/renamer.py
+++ b/renames/renamer.py
@@ -95,26 +95,45 @@ if __name__ == "__main__":
parser = argparse.ArgumentParser(description='Make replacements in files')
parser.add_argument('--reverse', action='store_true',
help='Performs replacements in the reverse direction')
- parser.add_argument('--renames-file', nargs=1,
- default=[renamesPath],
- help='file containing the replacements to perform (from -> to)')
+ parser.add_argument('--verbose', action='store_true',
+ help='More chatty about operations')
+ parser.add_argument('--no-specific', action='store_true',
+ help='Does not add specific renames when called without renames files')
+ parser.add_argument('--renames-file', nargs=1, action='append',
+ help='file containing the replacements to perform (from -> to), default is ' + renamesPath)
parser.add_argument('toRename', metavar='P', nargs='+',
help='path to a file to rename')
args = parser.parse_args()
+ if args.verbose:
+ logging.getLogger().setLevel(logging.DEBUG)
+ baseRenameFiles = []
+ specificRenames = {}
if not args.renames_file:
+ baseRenameFiles.append(renamesPath)
baseRenames = loadRenamesFile(renamesPath, args.reverse)
+ if not args.no_specific:
+ import glob
+ for r in glob.glob(os.path.join(os.path.dirname(renamesPath),"*.renames")):
+ key = os.path.basename(r[:-len('.renames')])
+ specificRenames[key] = loadRenamesFile(r, args.reverse)
+ logging.info("specificRenames:%s", specificRenames.keys())
else:
- baseRenames = loadRenamesFile(args.renames_file[0], args.reverse)
+ baseRenames = {}
+ for r in args.renames_file:
+ baseRenameFiles.append(r[0])
+ baseRenames.update(loadRenamesFile(r[0], args.reverse))
for f in args.toRename:
try:
- basename = os.path.splitext(os.path.splitext(os.path.basename(f))[0])[0]
- specificRenames = os.path.join(os.path.dirname(renamesPath), basename + ".renames")
- if not args.renames_file and os.path.exists(specificRenames):
- renames = loadRenamesFile(specificRenames, arg.reverse)
- renames.update(baseRenames)
- else:
- renames = baseRenames
+ specificFiles = []
+ renames = baseRenames
+ for skey, svals in specificRenames.items():
+ if skey.lower() in f.lower():
+ specificFiles.append(os.path.join(renamesPath, skey+'.renames'))
+ nrenames = {}
+ nrenames.update(renames)
+ nrenames.update(svals)
+ renames = nrenames
+ logging.info('%r: %r', f, baseRenameFiles + specificFiles)
replaceInFile(f, renames)
except:
logging.exception("handling file %s", f)
- print("DONE")
diff --git a/renames/renames.txt b/renames/renames.txt
index 9a27a5c97fac5e82d46cebeebd35c2046f7bad6f..cfcd68840762a3fb45ade210b672d8b94c8369e0 100644
--- a/renames/renames.txt
+++ b/renames/renames.txt
@@ -79,6 +79,28 @@ x_castep_Parameter_n -> x_castep_parameter_n
x_castep_SCF_frame_energy_gain -> x_castep_scf_frame_energy_gain
x_castep_Parameter_s6 -> x_castep_parameter_s6
x_castep_DFPT_solver_method -> x_castep_dfpt_solver_method
+frame_sequence_conserved_quantity -> xxx_conserved_quantity
+frame_sequence_conserved_quantity_frames -> xxx_to_rm_frame_sequence_conserved_quantity_frames
+conserved_quantity -> xxx_conserved_quantity
+frame_sequence_kinetic_energy -> xxx_kinetic_energy
+frame_sequence_local_frames_ref -> frame_sequence_to_frames_ref
+frame_sequence_potential_energy -> xxx_potential_energy
+frame_sequence_pressure -> xxx_instant_pressure
+frame_sequence_temperature -> xxx_instant_temperature
+frame_sequence_to_sampling_ref -> frame_sequence_to_sampling_method_ref
+frame_sequence_user_quantity_frames -> xxx_to_rm_frame_sequence_user_quantity_frames
+frame_sequence_user_quantity -> xxx_user_quantity
+frame_sequence_user_quantity_name -> xxx_user_quantity_name
+frame_sequence_user_quantity_stats -> xxx_user_quantity_stats
+number_of_frame_sequence_user_quantity_components -> xxx_user_quantity_components
+number_of_frame_sequence_user_quantity_evaluations_in_sequence -> xxx_to_rm_number_of_frame_sequence_user_quantity_evaluations_in_sequence
+frame_sequence_kinetic_energy_frames -> xxx_to_rm_frame_sequence_kinetic_energy_frames
+frame_sequence_potential_energy_frames -> xxx_to_rm_frame_sequence_potential_energy_frames
+frame_sequence_pressure_frames -> xxx_to_rm_frame_sequence_pressure_frames
+frame_sequence_temperature_frames -> xxx_to_rm_frame_sequence_temperature_frames
+section_frame_sequence_user_quantity -> xxx_user_quantity
+single_configuration_to_calculation_method_ref -> single_configuration_calculation_to_method_ref
+user_quantity_frames -> xxx_to_rm_user_quantity_frames
x_cp2k_energy_XC_scf_iteration -> x_cp2k_energy_xc_scf_iteration
x_fhi_aims_controlInOut_species_cut_pot -> x_fhi_aims_controlinout_species_cut_pot
x_fhi_aims_controlInOut_species_cut_pot_scale -> x_fhi_aims_controlinout_species_cut_pot_scale
diff --git a/renames/siesta_autogenerated.renames b/renames/siesta.renames
similarity index 100%
rename from renames/siesta_autogenerated.renames
rename to renames/siesta.renames