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Merge pull request #77 from ax3l/fix-np-2.0-fixed-size-str-1.1.X
Numpy 2.0: `np.string_` -> `np.bytes_`
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -37,8 +37,8 @@ def get_basePath(f, iteration): | |
| ------- | ||
| A string with a in-file path. | ||
| """ | ||
| iteration_str = np.string_(str(iteration)) | ||
| return np.string_(f.attrs["basePath"]).replace(b"%T", iteration_str) | ||
| iteration_str = np.bytes_(str(iteration)) | ||
| return np.bytes_(f.attrs["basePath"]).replace(b"%T", iteration_str) | ||
|
|
||
| def setup_base_path(f, iteration): | ||
| """ | ||
|
|
@@ -67,7 +67,7 @@ def get_software_dependencies(): | |
| Returns the software dependencies of this script as a semicolon | ||
| separated string. | ||
| """ | ||
| return np.string_( | ||
| return np.bytes_( | ||
| "python@{0}.{1}.{2};".format( | ||
| sys.version_info.major, | ||
| sys.version_info.minor, | ||
|
|
@@ -92,25 +92,25 @@ def setup_root_attr(f): | |
| ext_list = [["ED-PIC", np.uint32(1)]] | ||
|
|
||
| # Required attributes | ||
| f.attrs["openPMD"] = np.string_("1.1.0") | ||
| f.attrs["openPMD"] = np.bytes_("1.1.0") | ||
| f.attrs["openPMDextension"] = ext_list[0][1] # ED-PIC extension is used | ||
| f.attrs["basePath"] = np.string_("/data/%T/") | ||
| f.attrs["meshesPath"] = np.string_("meshes/") | ||
| f.attrs["particlesPath"] = np.string_("particles/") | ||
| f.attrs["iterationEncoding"] = np.string_("groupBased") | ||
| f.attrs["iterationFormat"] = np.string_("/data/%T/") | ||
| f.attrs["basePath"] = np.bytes_("/data/%T/") | ||
| f.attrs["meshesPath"] = np.bytes_("meshes/") | ||
| f.attrs["particlesPath"] = np.bytes_("particles/") | ||
| f.attrs["iterationEncoding"] = np.bytes_("groupBased") | ||
| f.attrs["iterationFormat"] = np.bytes_("/data/%T/") | ||
|
|
||
| # Recommended attributes | ||
| f.attrs["author"] = np.string_("Axel Huebl <[email protected]>") | ||
| f.attrs["software"] = np.string_("openPMD Example Script") | ||
| f.attrs["softwareVersion"] = np.string_("1.1.0.4") | ||
| f.attrs["author"] = np.bytes_("Axel Huebl <[email protected]>") | ||
| f.attrs["software"] = np.bytes_("openPMD Example Script") | ||
| f.attrs["softwareVersion"] = np.bytes_("1.1.0.4") | ||
| f.attrs["softwareDependencies"] = get_software_dependencies() | ||
| f.attrs["machine"] = np.string_(socket.gethostname()) | ||
| f.attrs["date"] = np.string_( | ||
| f.attrs["machine"] = np.bytes_(socket.gethostname()) | ||
| f.attrs["date"] = np.bytes_( | ||
| datetime.datetime.now(tzlocal()).strftime('%Y-%m-%d %H:%M:%S %z')) | ||
|
|
||
| # Optional | ||
| f.attrs["comment"] = np.string_("This is a dummy file for test purposes.") | ||
| f.attrs["comment"] = np.bytes_("This is a dummy file for test purposes.") | ||
|
|
||
|
|
||
| def write_rho_cylindrical(meshes, mode0, mode1): | ||
|
|
@@ -133,17 +133,17 @@ def write_rho_cylindrical(meshes, mode0, mode1): | |
| (The first axis corresponds to r, and the second axis corresponds to z) | ||
| """ | ||
| # Path to the rho meshes, within the h5py file | ||
| full_rho_path = np.string_("rho") | ||
| full_rho_path = np.bytes_("rho") | ||
| meshes.create_dataset( full_rho_path, (3, mode0.shape[0], mode0.shape[1]), \ | ||
| dtype=np.float32) | ||
| rho = meshes[full_rho_path] | ||
| rho.attrs["comment"] = np.string_( | ||
| rho.attrs["comment"] = np.bytes_( | ||
| "Density of electrons in azimuthal decomposition") | ||
|
|
||
| # Create the dataset (cylindrical with azimuthal modes up to m=1) | ||
| # The first axis has size 2m+1 | ||
| rho.attrs["geometry"] = np.string_("thetaMode") | ||
| rho.attrs["geometryParameters"] = np.string_("m=1; imag=+") | ||
| rho.attrs["geometry"] = np.bytes_("thetaMode") | ||
| rho.attrs["geometryParameters"] = np.bytes_("m=1; imag=+") | ||
|
|
||
| # Add information on the units of the data | ||
| rho.attrs["unitSI"] = np.float64(1.0) | ||
|
|
@@ -160,7 +160,7 @@ def write_rho_cylindrical(meshes, mode0, mode1): | |
| rho.attrs["gridGlobalOffset"] = np.array([0.0, 0.0], dtype=np.float32) | ||
| rho.attrs["position"] = np.array([0.0, 0.0], dtype=np.float32) | ||
| rho.attrs["gridUnitSI"] = np.float64(1.0) | ||
| rho.attrs["dataOrder"] = np.string_("C") | ||
| rho.attrs["dataOrder"] = np.bytes_("C") | ||
| rho.attrs["axisLabels"] = np.array([b"r",b"z"]) | ||
|
|
||
| # Add specific information for PIC simulations | ||
|
|
@@ -199,11 +199,11 @@ def write_b_2d_cartesian(meshes, data_ez): | |
| B.create_dataset(b"z", data_ez.shape, dtype=np.float32) | ||
|
|
||
| # Write the common metadata for the group | ||
| B.attrs["geometry"] = np.string_("cartesian") | ||
| B.attrs["geometry"] = np.bytes_("cartesian") | ||
| B.attrs["gridSpacing"] = np.array([1.0, 1.0], dtype=np.float32) # dx, dy | ||
| B.attrs["gridGlobalOffset"] = np.array([0.0, 0.0], dtype=np.float32) | ||
| B.attrs["gridUnitSI"] = np.float64(1.0) | ||
| B.attrs["dataOrder"] = np.string_("C") | ||
| B.attrs["dataOrder"] = np.bytes_("C") | ||
| B.attrs["axisLabels"] = np.array([b"x",b"y"]) | ||
| B.attrs["unitDimension"] = \ | ||
| np.array([0.0, 1.0, -2.0, -1.0, 0.0, 0.0, 0.0 ], dtype=np.float64) | ||
|
|
@@ -261,11 +261,11 @@ def write_e_2d_cartesian(meshes, data_ex, data_ey, data_ez ): | |
| E.create_dataset(b"z", data_ez.shape, dtype=np.float32) | ||
|
|
||
| # Write the common metadata for the group | ||
| E.attrs["geometry"] = np.string_("cartesian") | ||
| E.attrs["geometry"] = np.bytes_("cartesian") | ||
| E.attrs["gridSpacing"] = np.array([1.0, 1.0], dtype=np.float32) # dx, dy | ||
| E.attrs["gridGlobalOffset"] = np.array([0.0, 0.0], dtype=np.float32) | ||
| E.attrs["gridUnitSI"] = np.float64(1.0) | ||
| E.attrs["dataOrder"] = np.string_("C") | ||
| E.attrs["dataOrder"] = np.bytes_("C") | ||
| E.attrs["axisLabels"] = np.array([b"x",b"y"]) | ||
| E.attrs["unitDimension"] = \ | ||
| np.array([1.0, 1.0, -3.0, -1.0, 0.0, 0.0, 0.0 ], dtype=np.float64) | ||
|
|
@@ -307,9 +307,9 @@ def add_EDPIC_attr_meshes(field): | |
| and Dataset for scalar meshes) | ||
| """ | ||
| field.attrs["fieldSmoothing"] = np.string_("none") | ||
| field.attrs["fieldSmoothing"] = np.bytes_("none") | ||
| # field.attrs["fieldSmoothingParameters"] = \ | ||
| # np.string_("period=10;numPasses=4;compensator=true") | ||
| # np.bytes_("period=10;numPasses=4;compensator=true") | ||
|
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||
|
|
||
| def add_EDPIC_attr_particles(particle): | ||
|
|
@@ -324,13 +324,13 @@ def add_EDPIC_attr_particles(particle): | |
| """ | ||
| particle.attrs["particleShape"] = 3.0 | ||
| particle.attrs["currentDeposition"] = np.string_("Esirkepov") | ||
| # particle.attrs["currentDepositionParameters"] = np.string_("") | ||
| particle.attrs["particlePush"] = np.string_("Boris") | ||
| particle.attrs["particleInterpolation"] = np.string_("uniform") | ||
| particle.attrs["particleSmoothing"] = np.string_("none") | ||
| particle.attrs["currentDeposition"] = np.bytes_("Esirkepov") | ||
| # particle.attrs["currentDepositionParameters"] = np.bytes_("") | ||
| particle.attrs["particlePush"] = np.bytes_("Boris") | ||
| particle.attrs["particleInterpolation"] = np.bytes_("uniform") | ||
| particle.attrs["particleSmoothing"] = np.bytes_("none") | ||
| # particle.attrs["particleSmoothingParameters"] = \ | ||
| # np.string_("period=1;numPasses=2;compensator=false") | ||
| # np.bytes_("period=1;numPasses=2;compensator=false") | ||
|
|
||
|
|
||
| def write_meshes(f, iteration): | ||
|
|
@@ -339,15 +339,15 @@ def write_meshes(f, iteration): | |
| meshes = f[full_meshes_path] | ||
|
|
||
| # Extension: Additional attributes for ED-PIC | ||
| meshes.attrs["fieldSolver"] = np.string_("Yee") | ||
| meshes.attrs["fieldSolver"] = np.bytes_("Yee") | ||
| meshes.attrs["fieldBoundary"] = np.array( | ||
| [b"periodic", b"periodic", b"open", b"open"]) | ||
| meshes.attrs["particleBoundary"] = np.array( | ||
| [b"periodic", b"periodic", b"absorbing", b"absorbing"]) | ||
| meshes.attrs["currentSmoothing"] = np.string_("Binomial") | ||
| meshes.attrs["currentSmoothing"] = np.bytes_("Binomial") | ||
| meshes.attrs["currentSmoothingParameters"] = \ | ||
| np.string_("period=1;numPasses=2;compensator=false") | ||
| meshes.attrs["chargeCorrection"] = np.string_("none") | ||
| np.bytes_("period=1;numPasses=2;compensator=false") | ||
| meshes.attrs["chargeCorrection"] = np.bytes_("none") | ||
|
|
||
| # (Here the data is randomly generated, but in an actual simulation, | ||
| # this would be replaced by the simulation data.) | ||
|
|
@@ -375,7 +375,7 @@ def write_particles(f, iteration): | |
|
|
||
| globalNumParticles = 128 # example number of all particles | ||
|
|
||
| electrons.attrs["comment"] = np.string_("My first electron species") | ||
| electrons.attrs["comment"] = np.bytes_("My first electron species") | ||
|
|
||
| # Extension: ED-PIC Attributes | ||
| # required | ||
|
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||