This file contains the source code for PREFIDA
Check dict dec is formatted according to schema
schema: dict schema
dic: dict to check
err: error code
desc: description of dict dic
>>> dic = {'a':0, 'b':[1.d0,2.d0], 'c':"example"} >>> schema = {'a':{'dims':0,'type':[int]}, 'b':{'dims':[2],'type':[float, np.float64]}, 'c':{'dims':0,'type':[str]} } >>> err = check_dict_schema(schema, dic, desc="Example dict") >>> print(err) False
Checks if input dictionary is valid
inputs: input dictionary
inputs: Updated inputs dictionary
>>> inputs = check_inputs(inputs)
Checks if interpolation grid structure is valid
grid: Interpolation grid structure
>>> check_grid(grid)
Checks if neutral beam geometry dictionary is valid. Converts lists to numpy ndarrays
inputs: input dictionary
nbi: neutral beam geometry dictionary
nbi: Updated nbi dictionary
>>> nbi = check_beam(inputs, nbi)
Checks if plasma paramters dictionary is valid
inputs: Input dictionary
grid: Interpolation grid dictionary
plasma: Plasma parameters dictionary
plasma: Updated plasma dictionary
>>> plasma = check_plasma(inputs, grid, plasma)
Checks if electromagnetic fields dictionary is valid
inputs: Input dictionary
grid: Interpolation grid dictionary
fields: Electromagnetic fields dictionary
fields: Updated fields dictionary
>>> fields = check_fields(inputs, grid, fields)
Checks if distribution dictionary is valid
inputs: Input dictionary
grid: Interpolation grid dictionary
dist: Fast-ion distribution dictionary
dist: Updated dist dictionary
>>> dist = check_distribution(inputs, grid, dist)
Check if spectral geometry dictionary is valid
inputs: input dictionary
chords: spectral geometry dictionary
>>> check_spec(inputs, chords)
Checks if NPA geometry dictionary is valid
inputs: input dictionary
npa: NPA geometry dictionary
>>> check_npa(inputs, npa)
Writes namelist file
filename: Name of the namelist file
inputs: Input dictionary
>>> write_namelist(filename, inputs)
Write geometry values to a HDF5 file
filename: Name of the geometry file
nbi: NBI geometry structure
spec: Optional, Spectral geometry structure
npa: Optional, NPA geometry structure
>>> write_geometry(filename, nbi, spec=spec, npa=npa)
Write MHD equilibrium values to a HDF5 file
filename: Name of the equilibrium file
plasma: Plasma dictionary
fields: Electromagnetic fields dictionary
>>> write_equilibrium(filename, plasma, fields)
Write fast-ion distribution to a HDF5 file
filename: Name of the distribution file
dist: Fast-ion distribution distionary
>>> write_distribution(filename, distri)
Checks FIDASIM inputs and writes FIDASIM input files
inputs: Inputs structure
grid: Interpolation grid structure
nbi: Neutral beam geometry structure
plasma: Plasma parameters structure
fields: Electromagnetic fields structure
fbm: Fast-ion distribution structure
spec: Optional, Spectral geometry structure
npa: Optional, NPA geometry structure
>>> prefida(inputs, grid, nbi, plasma, fields, fbm, spec=spec, npa=npa)
#!/usr/bin/env python # -*- coding: utf-8 -*- #+#PREFIDA Source #+ This file contains the source code for PREFIDA #+*** from __future__ import print_function import os import numpy as np import datetime import h5py from fidasim.utils import * def check_dict_schema(schema, dic, desc=None): """ #+#check_dict_schema #+ Check dict `dec` is formatted according to `schema` #+*** #+##Input Arguments #+ **schema**: dict schema #+ #+ **dic**: dict to check #+ #+##Output Arguments #+ **err**: error code #+ #+##Keyword Arguments #+ **desc**: description of dict `dic` #+ #+##Example usage #+```python #+>>> dic = {'a':0, 'b':[1.d0,2.d0], 'c':"example"} #+>>> schema = {'a':{'dims':0,'type':[int]}, 'b':{'dims':[2],'type':[float, np.float64]}, 'c':{'dims':0,'type':[str]} } #+ #+>>> err = check_dict_schema(schema, dic, desc="Example dict") #+>>> print(err) #+ False #+``` """ if desc is None: desc = 'dict' err = False schema_keys = list(schema.keys()) dic_keys = list(dic.keys()) # Note extra variables for key in dic_keys: if key not in schema_keys: info('Extra variable "{}" found in "{}"'.format(key, desc)) for key in schema_keys: # Note missing data if key not in dic_keys: error('"{}" is missing from "{}"'.format(key, desc)) err = True else: # Check type if (schema[key]['dims'] == 0): if not isinstance(dic[key], tuple(schema[key]['type'])): error('"{}" has the wrong type of {}. Expected {}'.format(key, type(dic[key]), schema[key]['type'])) err = True elif dic[key].dtype.type not in schema[key]['type']: error('"{}" has the wrong type of {}. Expected {}'.format(key, dic[key].dtype.type, schema[key]['type'])) err = True # Check for NaNs or Inf if (not isinstance(dic[key], (str, dict, float, int))) and (np.bytes_ not in schema[key]['type']): if (dic[key][np.isnan(dic[key])].size > 0) or (dic[key][np.isinf(dic[key])].size > 0): error('NaN or Infinity detected in "{}"'.format(key)) err = True # Check shape if not np.array_equal(dic[key].shape, schema[key]['dims']): error('"{}" has the wrong shape of {}. Expected ({})'.format(key, dic[key].shape, schema[key]['dims'])) print('ndim({}) = {}'.format(key, dic[key].ndim)) err = True # Check shape if isinstance(dic[key], (str, int, float)): if (schema[key]['dims'] != 0) and (schema[key]['dims'] != [0]): error('"{}" has the wrong shape. Expected ({})'.format(key, schema[key]['dims'])) err = True return err def check_inputs(inputs): """ #+#check_inputs #+Checks if input dictionary is valid #+*** #+##Input Arguments #+ **inputs**: input dictionary #+ #+##Output Arguments #+ **inputs**: Updated inputs dictionary #+ #+##Example Usage #+```dist #+>>> inputs = check_inputs(inputs) #+``` """ info('Checking simulation settings...') err = False zero_string = {'dims': 0, 'type': [str]} zero_int = {'dims': 0, 'type': [int, np.int32, np.int64]} zero_long = {'dims': 0, 'type': [int, np.int32, np.int64]} zero_double = {'dims': 0, 'type': [float, np.float64]} three_double = {'dims': [3], 'type': [float, np.float64]} schema = {'comment': zero_string, 'shot': zero_long, 'time': zero_double, 'runid': zero_string, 'device': zero_string, 'tables_file': zero_string, 'result_dir': zero_string, 'nlambda': zero_int, 'lambdamin': zero_double, 'lambdamax': zero_double, 'nx': zero_int, 'ny': zero_int, 'nz': zero_int, 'alpha': zero_double, 'beta': zero_double, 'gamma': zero_double, 'origin': three_double, 'xmin': zero_double, 'xmax': zero_double, 'ymin': zero_double, 'ymax': zero_double, 'zmin': zero_double, 'zmax': zero_double, 'ab': zero_double, 'ai': zero_double, 'current_fractions': three_double, 'pinj': zero_double, 'einj': zero_double, 'impurity_charge': zero_int, 'n_fida': zero_long, 'n_nbi': zero_long, 'n_pfida': zero_long, 'n_pnpa': zero_long, 'n_dcx': zero_long, 'n_npa': zero_long, 'n_halo': zero_long, 'n_birth': zero_long, 'ne_wght': zero_int, 'np_wght': zero_int, 'nphi_wght': zero_int, 'emax_wght': zero_double, 'nlambda_wght': zero_int, 'lambdamin_wght': zero_double, 'lambdamax_wght': zero_double, 'calc_npa': zero_int, 'calc_fida': zero_int, 'calc_pnpa': zero_int, 'calc_pfida': zero_int, 'calc_bes': zero_int, 'calc_dcx': zero_int, 'calc_halo': zero_int, 'calc_cold': zero_int, 'calc_brems': zero_int, 'calc_birth': zero_int, 'calc_fida_wght': zero_int, 'calc_npa_wght': zero_int, 'calc_neutron': zero_int} err = check_dict_schema(schema, inputs, desc="simulation settings") if err: error('Invalid simulation settings. Exiting...', halt=True) # Normalize File Paths inputs['result_dir'] = os.path.abspath(inputs['result_dir']) if (inputs['alpha'] > 2. * np.pi) or (inputs['beta'] > 2. * np.pi) or (inputs['gamma'] > 2. * np.pi): error('Angles must be in radians') err = True if inputs['lambdamin'] >= inputs['lambdamax']: error('Invalid wavelength range. Expected lambdamin < lamdbdamax') err = True if inputs['lambdamin_wght'] >= inputs['lambdamax_wght']: error('Invalid wavelength range. Expected lambdamin_wght < lamdbdamax_wght') err = True if inputs['xmin'] >= inputs['xmax']: error('Invalid x range. Expected xmin < xmax') err = True if inputs['ymin'] >= inputs['ymax']: error('Invalid y range. Expected ymin < ymax') err = True if inputs['zmin'] >= inputs['zmax']: error('Invalid z range. Expected zmin < zmax') err = True if (inputs['pinj'] <= 0.) or (inputs['einj'] <= 0.0): error('The selected source is not on') print('einj = {}'.format(inputs['einj'])) print('pinj = {}'.format(inputs['pinj'])) err = True if np.abs(np.sum(inputs['current_fractions']) - 1.0) > 1e-3: error('current_fractions do not sum to 1.0') print('sum(current_fractions) = {}'.format(np.sum(inputs['current_fractions']))) err = True if inputs['impurity_charge'] <= 1: error('Invalid impurity charge. Expected impurity charge > 1') err = True ps = os.path.sep input_file = inputs['result_dir'] + ps + inputs['runid'] + '_inputs.dat' equilibrium_file = inputs['result_dir'] + ps + inputs['runid'] + '_equilibrium.h5' geometry_file = inputs['result_dir'] + ps + inputs['runid'] + '_geometry.h5' distribution_file = inputs['result_dir'] + ps + inputs['runid'] + '_distribution.h5' neutrals_file = inputs['result_dir'] + ps + inputs['runid'] + '_neutrals.h5' inputs['input_file'] = input_file inputs['equilibrium_file'] = equilibrium_file inputs['geometry_file'] = geometry_file inputs['distribution_file'] = distribution_file inputs['load_neutrals'] = 0 inputs['flr'] = 2 inputs['seed'] = -1 inputs['verbose'] = 1 inputs['neutrals_file'] = neutrals_file if err: error('Invalid simulation settings. Exiting...', halt=True) else: success('Simulation settings are valid') return inputs def check_grid(grid): """ #+#check_grid #+Checks if interpolation grid structure is valid #+*** #+##Input Arguments #+ **grid**: Interpolation grid structure #+ #+##Example Usage #+```python #+>>> check_grid(grid) #+``` """ err = False info('Checking interpolation grid...') if 'nr' not in grid: error('"nr" is missing from the interpolation grid') error('Invalid interpolation grid. Exiting...', halt=True) if 'nz' not in grid: error('"nz" is missing from the interpolation grid') error('Invalid interpolation grid. Exiting...', halt=True) if 'nphi' not in grid: info('"nphi" is missing from the interpolation grid, assuming axisymmetry') nphi =1 else: nphi = grid['nphi'] nr = grid['nr'] nz = grid['nz'] zero_int = {'dims': 0, 'type': [int, np.int32, np.int64]} nrnz_doub = {'dims': [nr, nz], 'type': [float, np.float64]} schema = {'nr': zero_int, 'nz': zero_int, 'nphi': zero_int, 'r2d': nrnz_doub, 'z2d': nrnz_doub, 'r': {'dims': [nr], 'type': [float, np.float64]}, 'z': {'dims': [nz], 'type': [float, np.float64]}, 'phi': {'dims': [nphi], 'type': [float, np.float64]}} err = check_dict_schema(schema, grid, desc="interpolation grid") if err: error('Invalid interpolation grid. Exiting...', halt=True) if not np.array_equal(grid['r'], np.sort(grid['r'])): error('r is not in ascending order') err = True if not np.array_equal(grid['z'], np.sort(grid['z'])): error('z is not in ascending order') err = True if not np.array_equal(grid['r'], grid['r2d'][:, 0]): error('r2d is defined incorrectly. Expected r == r2d[:, 0]') err = True if not np.array_equal(grid['z'], grid['z2d'][0, :]): error('z2d is defined incorrectly. Expected z == z2d[0, :]') err = True if err: error('Invalid interpolation grid. Exiting...', halt=True) else: success('Interpolation grid is valid') def check_beam(inputs, nbi): """ #+#check_beam #+Checks if neutral beam geometry dictionary is valid. Converts lists to numpy ndarrays #+*** #+##Input Arguments #+ **inputs**: input dictionary #+ #+ **nbi**: neutral beam geometry dictionary #+ #+##Output Arguments #+ **nbi**: Updated nbi dictionary #+ #+##Example Usage #+```python #+>>> nbi = check_beam(inputs, nbi) #+``` """ err = False info('Checking beam geometry...') na = nbi['naperture'] zero_string = {'dims': 0, 'type': [str]} zero_int = {'dims': 0, 'type': [int, np.int32, np.int64]} zero_double = {'dims': 0, 'type': [float, np.float64]} three_double = {'dims': [3], 'type': [float, np.float64]} na_double = {'dims': [na], 'type': [float, np.float64]} na_int = {'dims': [na], 'type': [int, np.int32, np.int64]} schema = {'data_source': zero_string, 'name': zero_string, 'shape': zero_int, 'src': three_double, 'axis': three_double, 'divy': three_double, 'divz': three_double, 'focy': zero_double, 'focz': zero_double, 'widz': zero_double, 'widy': zero_double} # Add to schema if aperatures are present if nbi['naperture'] > 0: schema['naperture'] = zero_int schema['ashape'] = na_int schema['awidy'] = na_double schema['awidz'] = na_double schema['aoffy'] = na_double schema['aoffz'] = na_double schema['adist'] = na_double # Convert to np arrays for indexing nbi['ashape'] = np.array(nbi['ashape'], dtype=int, ndmin=1) nbi['awidy'] = np.array(nbi['awidy'], dtype=float, ndmin=1) nbi['awidz'] = np.array(nbi['awidz'], dtype=float, ndmin=1) nbi['aoffy'] = np.array(nbi['aoffy'], dtype=float, ndmin=1) nbi['aoffz'] = np.array(nbi['aoffz'], dtype=float, ndmin=1) nbi['adist'] = np.array(nbi['adist'], dtype=float, ndmin=1) err = check_dict_schema(schema, nbi, desc="beam geometry") if err: error('Invalid beam geometry. Exiting...', halt=True) if np.abs(np.sum(nbi['axis'] ** 2.) - 1.) > 1e-5: error('Invalid source axis. Expected norm(axis) == 1') err = True if nbi['focz'] <= 0.0: error('focz cannot be in the range (-Inf,0.0]') err = True if nbi['focy'] <= 0.0: error('focy cannot be in the range (-Inf,0.0]') err = True if nbi['shape'] not in [1, 2]: error('Invalid source shape. Expected 1 (rectagular) or 2 (circular)') err = True if nbi['widz'] < 0.: error('Invalid widz. Expected widz > 0') err = True if nbi['widy'] < 0: error('Invalid widy. Expected widy > 0') err = True if nbi['naperture'] > 0: if nbi['ashape'] not in [1, 2]: error('Invalid aperture shape. Expected 1 (rectangular) or 2 (circular)') err = True w = nbi['awidy'] < 0 nw = len(nbi['awidy'][w]) if nw > 0: error('Invalid awidy. Expected awidy >= 0.0') err = True w = nbi['awidz'] < 0 nw = len(nbi['awidz'][w]) if nw > 0: error('Invalid awidz. Expected awidz >= 0.0') err = True # Machine coordinates origin = inputs['origin'] uvw_src = nbi['src'] uvw_axis = nbi['axis'] if nbi['naperture'] == 0: uvw_pos = uvw_src + 100 * uvw_axis else: uvw_pos = uvw_src + nbi['adist'][0] # Convert to beam coordinates xyz_src = uvw_to_xyz(inputs['alpha'], inputs['beta'], inputs['gamma'], uvw_src, origin=origin) xyz_axis = uvw_to_xyz(inputs['alpha'], inputs['beta'], inputs['gamma'], uvw_axis) xyz_pos = uvw_to_xyz(inputs['alpha'], inputs['beta'], inputs['gamma'], uvw_pos, origin=origin) xyz_center = uvw_to_xyz(inputs['alpha'], inputs['beta'], inputs['gamma'], [0., 0., 0.], origin=origin) dis = np.sqrt(np.sum((xyz_src - xyz_pos) ** 2.)) alpha = np.arctan2((xyz_pos[1] - xyz_src[1]), (xyz_pos[0] - xyz_src[0])) beta = np.arcsin((xyz_src[2] - xyz_pos[2]) / dis) print('Machine center in beam grid coordinates') print(xyz_center) print('Beam injection start point in machine coordinates') print(uvw_src) print('Beam injection start point in beam grid coordinates') print(xyz_src) if nbi['naperture'] != 0: print('First aperture position in machine coordinates') print(uvw_pos) print('First aperture position in beam grid coordinates') print(xyz_pos) else: print('Position of point 100cm along beam centerline in machine coordinates') print(uvw_pos) print('Position of point 100cm along beam centerline in beam grid coordinates') print(xyz_pos) print('Beam grid rotation angles that would align it with the beam centerline') print('alpha = {} deg.'.format(alpha / np.pi * 180.)) print('beta = {} deg.'.format(beta / np.pi * 180.)) # Calculate grid center rc and sides length dr dr = np.array([inputs['xmax'] - inputs['xmin'], inputs['ymax'] - inputs['ymin'], inputs['zmax'] - inputs['zmin']], dtype=np.float64) rc = np.array([inputs['xmin'], inputs['ymin'], inputs['zmin']], dtype=np.float64) + 0.5 * dr # Check if beam centerline intersects beam grid length, r_enter, r_exit = aabb_intersect(rc, dr, xyz_src, xyz_axis) print('Beam centerline - grid intersection length') print(length) if length <= 10.0: error('Beam centerline does not intersect grid') err = True if err: error('Invalid beam geometry. Exiting...', halt=True) else: success('Beam geometry is valid') return nbi def check_plasma(inputs, grid, plasma): """ #+#check_plasma #+Checks if plasma paramters dictionary is valid #+*** #+##Input Arguments #+ **inputs**: Input dictionary #+ #+ **grid**: Interpolation grid dictionary #+ #+ **plasma**: Plasma parameters dictionary #+ #+##Output Arguments #+ **plasma**: Updated plasma dictionary #+ #+##Example Usage #+```python #+>>> plasma = check_plasma(inputs, grid, plasma) #+``` """ err = False info('Checking plasma parameters...') nr = grid['nr'] nz = grid['nz'] if 'nphi' not in grid: info('"nphi" is missing from the plasma, assuming axisymmetry') nphi =1 else: nphi = grid['nphi'] zero_string = {'dims': 0, 'type': [str]} zero_double = {'dims': 0, 'type': [float, np.float64]} if nphi>1: nrnznphi_double = {'dims': [nr, nz, nphi], 'type': [float, np.float64, np.float64]} nrnznphi_int = {'dims': [nr, nz, nphi], 'type': [np.int64]} else: nrnznphi_double = {'dims': [nr, nz], 'type': [float, np.float64]} nrnznphi_int = {'dims': [nr, nz], 'type': [np.int64]} schema = {'time': zero_double, 'vr': nrnznphi_double, 'vt': nrnznphi_double, 'vz': nrnznphi_double, 'dene': nrnznphi_double, 'denn': nrnznphi_double, 'ti': nrnznphi_double, 'te': nrnznphi_double, 'zeff': nrnznphi_double, 'mask': nrnznphi_int, 'data_source': zero_string} err = check_dict_schema(schema, plasma, desc="plasma parameters") if err: error('Invalid plasma parameters. Exiting...', halt=True) if plasma['data_source'] == '': error('Invalid data source. An empty string is not a data source.') err = True # Electron density w = (plasma['dene'] < 0.) plasma['dene'][w] = 0. # Zeff w = (plasma['zeff'] < 1.) plasma['zeff'][w] = 1. # Electron temperature w = (plasma['te'] < 0.) plasma['te'][w] = 0. # Ion temperature w = (plasma['ti'] < 0.) plasma['ti'][w] = 0. if (np.abs(plasma['time'] - inputs['time']) > 0.02): warn('Plasma time and input time do not match') print('Input time: ', inputs['time']) print('Plasma time: ', plasma['time']) # Add grid elements to plasma dict plasma.update(grid.copy()) if err: error('Invalid plasma parameters. Exiting...', halt=True) else: success('Plasma parameters are valid') return plasma def check_fields(inputs, grid, fields): """ #+#check_fields #+Checks if electromagnetic fields dictionary is valid #+*** #+##Input Arguments #+ **inputs**: Input dictionary #+ #+ **grid**: Interpolation grid dictionary #+ #+ **fields**: Electromagnetic fields dictionary #+ #+##Output Arguments #+ **fields**: Updated fields dictionary #+ #+##Example Usage #+```python #+>>> fields = check_fields(inputs, grid, fields) #+``` """ err = False info('Checking electromagnetic fields...') nr = grid['nr'] nz = grid['nz'] if 'nphi' not in grid: info('"nphi" is missing from the fields, assuming axisymmetry') nphi =1 else: nphi = grid['nphi'] zero_string = {'dims': 0, 'type': [str]} zero_double = {'dims': 0, 'type': [float, np.float64]} if nphi>1: nrnznphi_double = {'dims': [nr, nz, nphi], 'type': [float, np.float64, np.float64]} nrnznphi_int = {'dims': [nr, nz, nphi], 'type': [int, np.int32, np.int64]} else: nrnznphi_double = {'dims': [nr, nz], 'type': [float, np.float64]} nrnznphi_int = {'dims': [nr, nz], 'type': [int, np.int32]} schema = {'time': zero_double, 'br': nrnznphi_double, 'bt': nrnznphi_double, 'bz': nrnznphi_double, 'er': nrnznphi_double, 'et': nrnznphi_double, 'ez': nrnznphi_double, 'mask': nrnznphi_int, 'data_source': zero_string} err = check_dict_schema(schema, fields, desc="electromagnetic fields") if err: error('Invalid electromagnetic fields. Exiting...', halt=True) if fields['data_source'] == '': error('Invalid data source. An empty string is not a data source.') err = True if np.abs(fields['time'] - inputs['time']) > 0.02: warn('Electromagnetic fields time and input time do not match') print('Input time: {}'.format(inputs['time'])) print('Electromagnetic fields time: {}'.format(fields['time'])) # Add grid elements to fields dict fields.update(grid.copy()) if err: error('Invalid electromagnetic fields. Exiting...', halt=True) else: success('Electromagnetic fields are valid') return fields def check_distribution(inputs, grid, dist): """ #+#check_distribution #+Checks if distribution dictionary is valid #+*** #+##Input Arguments #+ **inputs**: Input dictionary #+ #+ **grid**: Interpolation grid dictionary #+ #+ **dist**: Fast-ion distribution dictionary #+ #+##Output Arguments #+ **dist**: Updated dist dictionary #+ #+##Example Usage #+```python #+>>> dist = check_distribution(inputs, grid, dist) #+``` """ err = False info('Checking fast-ion distribution...') dist_keys = list(dist.keys()) if 'type' not in dist_keys: error('"type" is missing from the fast-ion distribution') error('Invalid fast-ion distribution. Exiting...', halt=True) dist_type = dist['type'] if dist_type == 1: print('Using a Guiding Center Fast-ion Density Function') if 'nenergy' not in dist_keys: error('"nenergy" is missing from the fast-ion distribution') error('Invalid fast-ion distribution. Exiting...', halt=True) if 'npitch' not in dist_keys: error('"npitch" is missing from the fast-ion distribution') error('Invalid fast-ion distribution. Exiting...', halt=True) npitch = dist['npitch'] nen = dist['nenergy'] nr = grid['nr'] nz = grid['nz'] if 'nphi' not in grid: info('"nphi" is missing from the fast-ion distribution, assuming axisymmetry') nphi =1 else: nphi = grid['nphi'] zero_string = {'dims': 0, 'type': [str]} zero_int = {'dims': 0, 'type': [int, np.int32, np.int64]} zero_double = {'dims': 0, 'type': [float, np.float64]} if nphi>1: nrnznphi_double = {'dims': [nr, nz, nphi], 'type': [float, np.float64, np.float64]} else: nrnznphi_double = {'dims': [nr, nz], 'type': [float, np.float64]} schema = {'type': zero_int, 'nenergy': zero_int, 'npitch': zero_int, 'energy': {'dims': [nen], 'type': [float, np.float64]}, 'pitch': {'dims': [npitch], 'type': [float, np.float64]}, 'denf': nrnznphi_double, 'time': zero_double, 'data_source': zero_string} if nphi>1: schema['f'] = {'dims': [nen, npitch, nr, nz, nphi], 'type': [float, np.float64]} else: schema['f'] = {'dims': [nen, npitch, nr, nz], 'type': [float, np.float64]} err = check_dict_schema(schema, dist, desc="fast-ion distribution") if err: error('Invalid fast-ion distribution. Exiting...', halt=True) # Add grid elements to plasma dict dist.update(grid.copy()) elif dist_type == 2: print('Using Guiding Center Monte Carlo fast-ion distribution') if 'nparticle' not in dist_keys: error('"nparticle" is missing from the fast-ion distribution') error('Invalid fast-ion distribution. Exiting...', halt=True) npart = dist['nparticle'] zero_int = {'dims': 0, 'type': [int, np.int32, np.int64]} zero_long = {'dims': 0, 'type': [int, np.int32, np.int64]} zero_string = {'dims': 0, 'type': [str]} zero_double = {'dims': 0, 'type':[float, np.float64]} npart_double = {'dims': [npart], 'type': [float, np.float64]} npart_int = {'dims': [npart], 'type': [int, np.int32, np.int64]} schema = {'type': zero_int, 'nparticle': zero_long, 'nclass': zero_int, 'time': zero_double, 'energy': npart_double, 'pitch': npart_double, 'r': npart_double, 'z': npart_double, 'weight': npart_double, 'class': npart_int, 'data_source': zero_string} err = check_dict_schema(schema, dist, desc="fast-ion distribution") if err: error('Invalid fast-ion distribution. Exiting...', halt=True) print('Number of MC particles: {}'.format(npart)) elif dist_type == 3: print('Using Full Orbit Monte Carlo fast-ion distribution') if 'nparticle' not in dist_keys: error('"nparticle" is missing from the fast-ion distribution') error('Invalid fast-ion distribution. Exiting...', halt=True) npart = dist['nparticle'] zero_int = {'dims': 0, 'type': [int, np.int32, np.int64]} zero_long = {'dims': 0, 'type': [int, np.int32, np.int64]} zero_string = {'dims': 0, 'type': [str]} zero_double = {'dims': 0, 'type': [float, np.float64]} npart_double = {'dims': [npart], 'type': [float, np.float64]} npart_int = {'dims': [npart], 'type': [int, np.int32, np.int64]} schema = {'type': zero_int, 'nparticle': zero_long, 'nclass': zero_int, 'time': zero_double, 'vr': npart_double, 'vt': npart_double, 'vz': npart_double, 'r': npart_double, 'z': npart_double, 'weight': npart_double, 'class': npart_int, 'data_source': zero_string} err = check_dict_schema(schema, dist, desc="fast-ion distribution") if err: error('Invalid fast-ion distribution. Exiting...', halt=True) print('Number of MC particles: {}'.format(npart)) else: error('Invalid distribution type. Expected ' + '1 (Guiding Center Density Function), ' + '2 (Guiding Center Monte Carlo), or ' + '3 (Full Orbit Monte Carlo)') error('Invalid fast-ion distribution. Exiting...', halt=True) if dist['data_source'] == '': error('Invalid data source. An empty string is not a data source.') err = True if np.abs(dist['time'] - inputs['time']) > 0.02: warn('Distribution time and input time do not match') print('Input time: {}'.format(inputs['time'])) print('Distribution time: {}'.format(dist['time'])) if err: error('Invalid fast-ion distribution. Exiting...', halt=True) else: success('Fast-ion distribution is valid') return dist def check_spec(inputs, chords): """ #+#check_spec #+Check if spectral geometry dictionary is valid #+*** #+##Input Arguments #+ **inputs**: input dictionary #+ #+ **chords**: spectral geometry dictionary #+ #+##Example Usage #+```python #+>>> check_spec(inputs, chords) #+``` """ err = False info('Checking FIDA/BES inputs...') chords_keys = list(chords.keys()) if 'nchan' not in chords_keys: error('"nchan" is missing from the FIDA/BES geometry') err = True error('Invalid FIDA/BES geometry. Exiting...', halt=True) nchan = chords['nchan'] zero_string = {'dims': 0, 'type': [str]} zero_long = {'dims': 0, 'type': [int, np.int32, np.int64]} nchan_double = {'dims': [nchan], 'type': [float, np.float64]} nchan_string = {'dims': [nchan], 'type': [np.bytes_, str]} three_nchan_float = {'dims': [3, nchan], 'type': [float, np.float64]} schema = {'data_source': zero_string, 'nchan': zero_long, 'system': zero_string, 'id': nchan_string, 'lens': three_nchan_float, 'axis': three_nchan_float, 'sigma_pi': nchan_double, 'spot_size': nchan_double, 'radius': nchan_double} err = check_dict_schema(schema, chords, desc="FIDA/BES geometry") if err: error('Invalid FIDA/BES geometry. Exiting...', halt=True) cross_arr = np.zeros(nchan, dtype=int) uvw_lens = chords['lens'] uvw_axis = chords['axis'] # ROTATE CHORDS INTO BEAM GRID COORDINATES xyz_lens = uvw_to_xyz(inputs['alpha'], inputs['beta'], inputs['gamma'], uvw_lens, origin=inputs['origin']) xyz_axis = uvw_to_xyz(inputs['alpha'], inputs['beta'], inputs['gamma'], uvw_axis) # Calculate grid center rc and sides length dr dr = np.array([inputs['xmax'] - inputs['xmin'], inputs['ymax'] - inputs['ymin'], inputs['zmax'] - inputs['zmin']], dtype=float) rc = np.array([inputs['xmin'], inputs['ymin'], inputs['zmin']], dtype=float) + 0.5 * dr for i in range(nchan): if not np.isclose(np.linalg.norm(uvw_axis[:, i]), 1, rtol=1e-03): error('Invalid optical axis for chord "' + str(chords['id'][i]) + '". Expected norm(axis) == 1') print(np.sum(uvw_axis[:, i] ** 2.)) # Check if viewing chord intersects beam grid length, r_enter, r_exit = aabb_intersect(rc, dr, xyz_lens[:, i], xyz_axis[:, i]) if length <= 0.0: cross_arr[i] = 1 wbad = (cross_arr == 1) nbad = cross_arr[wbad].size if nbad > 0: warn('The following {} chords do not cross the beam grid:'.format(nbad)) warn('Chord ID: {}'.format(chords['id'][wbad])) wgood = (cross_arr == 0) ngood = cross_arr[wgood].size print('{} out of {} chords crossed the beam grid'.format(ngood, nchan)) if ngood == 0: error('No channels intersect the beam grid') err = True if err: error('Invalid FIDA/BES geometry. Exiting...', halt=True) else: success('FIDA/BES geometry is valid') def check_npa(inp, npa): """ #+#check_npa #+Checks if NPA geometry dictionary is valid #+*** #+##Input Arguments #+ **inputs**: input dictionary #+ #+ **npa**: NPA geometry dictionary #+ #+##Example Usage #+```python #+>>> check_npa(inputs, npa) #+``` """ err = False info('Checking NPA geometry...') npa_keys = npa.keys() if 'nchan' not in npa_keys: error('"nchan" is missing from the NPA geometry') err = True error('Invalid NPA geometry. Exiting...', halt=True) nchan = npa['nchan'] zero_string = {'dims': 0, 'type': [str]} zero_long = {'dims': 0, 'type': [int, np.int32, np.int64]} three_float = {'dims': [3, nchan], 'type': [float, np.float64]} nchan_int = {'dims': [nchan], 'type': [int, np.int32, np.int64]} nchan_float = {'dims': [nchan], 'type': [float, np.float64]} nchan_string = {'dims': [nchan], 'type': [np.bytes_]} schema = {'data_source': zero_string, 'nchan': zero_long, 'system': zero_string, 'id': nchan_string, 'a_shape': nchan_int, 'd_shape': nchan_int, 'a_tedge': three_float, 'a_redge': three_float, 'a_cent': three_float, 'd_tedge': three_float, 'd_redge': three_float, 'd_cent': three_float, 'radius': nchan_float} err = check_dict_schema(schema, npa, desc="NPA geometry") if err: error('Invalid NPA geometry. Exiting...', halt=True) # Check detector/aperture shape w = np.logical_or(npa['d_shape'] > 2, npa['d_shape'] == 0) nw = len(npa['d_shape'][w]) if nw != 0: error('Invalid detector shape. Expected 1 (rectagular) or 2 (circular)') print('Invalid indices: {}'.format(np.arange(len(npa['d_shape']))[w])) err = True w = np.logical_or(npa['a_shape'] > 2, npa['a_shape'] == 0) nw = len(npa['a_shape'][w]) if nw != 0: error('Invalid aperture shape. Expected 1 (rectagular) or 2 (circular)') print('Invalid indices: {}'.format(np.arange(len(npa['a_shape']))[w])) err = True # Calculate grid center rc and sides length dr dr = np.array([inp['xmax'] - inp['xmin'], inp['ymax'] - inp['ymin'], inp['zmax'] - inp['zmin']]) rc = np.array([inp['xmin'], inp['ymin'], inp['zmin']]) + 0.5 * dr err_arr = np.zeros(nchan, dtype=int) for i in range(nchan): uvw_det = npa['d_cent'][:, i] d_e1 = npa['d_redge'][:, i] - uvw_det d_e2 = npa['d_tedge'][:, i] - uvw_det uvw_aper = npa['a_cent'][:, i] a_e1 = npa['a_redge'][:, i] - uvw_aper a_e2 = npa['a_tedge'][:, i] - uvw_aper uvw_dir = uvw_aper - uvw_det #Rotate chords into beam grid coordinates xyz_aper = uvw_to_xyz(inp['alpha'], inp['beta'], inp['gamma'], uvw_aper, origin=inp['origin']) xyz_det = uvw_to_xyz(inp['alpha'], inp['beta'], inp['gamma'], uvw_det, origin=inp['origin']) xyz_dir = xyz_aper - xyz_det xyz_dir = xyz_dir / np.sqrt(np.sum(xyz_dir * xyz_dir)) # Check if npa chord intersects beam grid length, r_enter, r_exit = aabb_intersect(rc, dr, xyz_det, xyz_dir) if length <= 0.: err_arr[i] = 1 # Check if NPA detector is pointing in the right direction d_enter = np.sqrt(np.sum((r_enter - xyz_aper)**2)) d_exit = np.sqrt(np.sum((r_exit - xyz_aper)**2)) if d_exit < d_enter: err_arr[i] = 1 # Check that the detector and aperture point in the same direction d_e3 = np.cross(d_e1, d_e2) a_e3 = np.cross(a_e1, a_e2) a_dp = np.sum(uvw_dir*a_e3) d_dp = np.sum(uvw_dir*d_e3) dp = np.sum(d_e3 * a_e3) if (dp <= 0.) or (a_dp <= 0.) or (d_dp <= 0.): error('The detector and/or aperture plane normal vectors are pointing in the wrong direction. The NPA definition is incorrect.') err_arr[i] = 1 w = (err_arr == 0) nw = err_arr[w].size ww = (err_arr != 0) nww = err_arr[ww].size print('{} out of {} channels crossed the beam grid'.format(nw, nchan)) if nw == 0: error('No channels intersect the beam grid') err = True if nww > 0: warn('Some channels did not intersect the beam grid') print('Number missed: {}'.format(nww)) print('Missed channels:') print(' {}'.format(npa['id'][ww])) if err: error('Invalid NPA geometry. Exiting...', halt=True) else: success('NPA geometry is valid') def write_namelist(filename, inputs): """ #+#write_namelist #+Writes namelist file #+*** #+##Input Arguments #+ **filename**: Name of the namelist file #+ #+ **inputs**: Input dictionary #+ #+##Example Usage #+```python #+>>> write_namelist(filename, inputs) #+``` """ info("Writing namelist file...") fidasim_version = get_version(get_fidasim_dir()) with open(filename, "w") as f: f.write("!! Created: {}\n".format(datetime.datetime.now())) f.write("!! FIDASIM version: {}\n".format(fidasim_version)) f.write("!! Comment: {}\n".format(inputs['comment'])) f.write("&fidasim_inputs\n\n") f.write("!! Shot Info\n") f.write("shot = {:d} !! Shot Number\n".format(inputs['shot'])) f.write("time = {:f} !! Time [s]\n".format(inputs['time'])) f.write("runid = '{}' !! runID\n".format(inputs['runid'])) f.write("result_dir = '{}' !! Result Directory\n\n".format(inputs['result_dir'])) f.write("!! Input Files\n") f.write("tables_file = '{}' !! Atomic Tables File\n".format(inputs['tables_file'])) f.write("equilibrium_file = '" + inputs['equilibrium_file'] + "' !! File containing plasma parameters and fields\n") f.write("geometry_file = '" + inputs['geometry_file'] + "' !! File containing NBI and diagnostic geometry\n") f.write("distribution_file = '" + inputs['distribution_file'] + "' !! File containing fast-ion distribution\n\n") f.write("!! Simulation Switches\n") f.write("calc_bes = {:d} !! Calculate NBI Spectra\n".format(inputs['calc_bes'])) f.write("calc_dcx = {:d} !! Calculate Direct CX Spectra\n".format(inputs['calc_dcx'])) f.write("calc_halo = {:d} !! Calculate Halo Spectra\n".format(inputs['calc_halo'])) f.write("calc_cold = {:d} !! Calculate Cold D-alpha Spectra\n".format(inputs['calc_cold'])) f.write("calc_brems = {:d} !! Calculate Bremsstrahlung\n".format(inputs['calc_brems'])) f.write("calc_fida = {:d} !! Calculate FIDA Spectra\n".format(inputs['calc_fida'])) f.write("calc_npa = {:d} !! Calculate NPA\n".format(inputs['calc_npa'])) f.write("calc_pfida = {:d} !! Calculate Passive FIDA Spectra\n".format(inputs['calc_pfida'])) f.write("calc_pnpa = {:d} !! Calculate Passive NPA\n".format(inputs['calc_pnpa'])) f.write("calc_neutron = {:d} !! Calculate B-T Neutron Rate\n".format(inputs['calc_neutron'])) f.write("calc_birth = {:d} !! Calculate Birth Profile\n".format(inputs['calc_birth'])) f.write("calc_fida_wght = {:d} !! Calculate FIDA weights\n".format(inputs['calc_fida_wght'])) f.write("calc_npa_wght = {:d} !! Calculate NPA weights\n".format(inputs['calc_npa_wght'])) f.write("!! Debugging Switches\n") f.write("seed = {:d} !! RNG Seed. If seed is negative a random seed is used\n".format(inputs['seed'])) f.write("flr = {:d} !! Turn on Finite Larmor Radius corrections\n".format(inputs['flr'])) f.write("load_neutrals = {:d} !! Load neutrals from neutrals file\n".format(inputs['load_neutrals'])) f.write("neutrals_file = '" + inputs['neutrals_file'] + "' !! File containing the neutral density\n") f.write("verbose = {:d} !! Verbose\n\n".format(inputs['verbose'])) f.write("!! Monte Carlo Settings\n") f.write("n_fida = {:d} !! Number of FIDA mc particles\n".format(inputs['n_fida'])) f.write("n_npa = {:d} !! Number of NPA mc particles\n".format(inputs['n_npa'])) f.write("n_pfida = {:d} !! Number of Passive FIDA mc particles\n".format(inputs['n_pfida'])) f.write("n_pnpa = {:d} !! Number of Passive NPA mc particles\n".format(inputs['n_pnpa'])) f.write("n_nbi = {:d} !! Number of NBI mc particles\n".format(inputs['n_nbi'])) f.write("n_halo = {:d} !! Number of HALO mc particles\n".format(inputs['n_halo'])) f.write("n_dcx = {:d} !! Number of DCX mc particles\n".format(inputs['n_dcx'])) f.write("n_birth = {:d} !! Number of BIRTH mc particles\n\n".format(inputs['n_birth'])) f.write("!! Neutral Beam Settings\n") f.write("ab = {:f} !! Beam Species mass [amu]\n".format(inputs['ab'])) f.write("pinj = {:f} !! Beam Power [MW]\n".format(inputs['pinj'])) f.write("einj = {:f} !! Beam Energy [keV]\n".format(inputs['einj'])) f.write("current_fractions(1) = {:f} !! Current Fractions (Full component)\n".format(inputs['current_fractions'][0])) f.write("current_fractions(2) = {:f} !! Current Fractions (Half component)\n".format(inputs['current_fractions'][1])) f.write("current_fractions(3) = {:f} !! Current Fractions (Third component)\n\n".format(inputs['current_fractions'][2])) f.write("!! Plasma Settings\n") f.write("ai = {:f} !! Ion Species mass [amu]\n".format(inputs['ai'])) f.write("impurity_charge = {:d} !! Impurity Charge\n\n".format(inputs['impurity_charge'])) f.write("!! Beam Grid Settings\n") f.write("nx = {:d} !! Number of cells in X direction (Into Plasma)\n".format(inputs['nx'])) f.write("ny = {:d} !! Number of cells in Y direction\n".format(inputs['ny'])) f.write("nz = {:d} !! Number of cells in Z direction\n".format(inputs['nz'])) f.write("xmin = {:f} !! Minimum X value [cm]\n".format(inputs['xmin'])) f.write("xmax = {:f} !! Maximum X value [cm]\n".format(inputs['xmax'])) f.write("ymin = {:f} !! Minimum Y value [cm]\n".format(inputs['ymin'])) f.write("ymax = {:f} !! Maximum Y value [cm]\n".format(inputs['ymax'])) f.write("zmin = {:f} !! Minimum Z value [cm]\n".format(inputs['zmin'])) f.write("zmax = {:f} !! Maximum Z value [cm]\n\n".format(inputs['zmax'])) f.write("!! Tait-Bryan Angles for z-y`-x`` rotation\n") f.write("alpha = {:f} !! Rotation about z-axis [rad]\n".format(inputs['alpha'])) f.write("beta = {:f} !! Rotation about y`-axis [rad]\n".format(inputs['beta'])) f.write("gamma = {:f} !! Rotation about x``-axis [rad]\n\n".format(inputs['gamma'])) f.write("!! Beam Grid origin in machine coordinates (cartesian)\n") f.write("origin(1) = {:f} !! U value [cm]\n".format(inputs['origin'][0])) f.write("origin(2) = {:f} !! V value [cm]\n".format(inputs['origin'][1])) f.write("origin(3) = {:f} !! W value [cm]\n\n".format(inputs['origin'][2])) f.write("!! Wavelength Grid Settings\n") f.write("nlambda = {:d} !! Number of Wavelengths\n".format(inputs['nlambda'])) f.write("lambdamin = {:f} !! Minimum Wavelength [nm]\n".format(inputs['lambdamin'])) f.write("lambdamax = {:f} !! Maximum Wavelength [nm]\n\n".format(inputs['lambdamax'])) f.write("!! Weight Function Settings\n") f.write("ne_wght = {:d} !! Number of Energies for Weights\n".format(inputs['ne_wght'])) f.write("np_wght = {:d} !! Number of Pitches for Weights\n".format(inputs['np_wght'])) f.write("nphi_wght = {:d} !! Number of Gyro-angles for Weights\n".format(inputs['nphi_wght'])) f.write("emax_wght = {:f} !! Maximum Energy for Weights [keV]\n".format(inputs['emax_wght'])) f.write("nlambda_wght = {:d} !! Number of Wavelengths for Weights \n".format(inputs['nlambda_wght'])) f.write("lambdamin_wght = {:f} !! Minimum Wavelength for Weights [nm]\n".format(inputs['lambdamin_wght'])) f.write("lambdamax_wght = {:f} !! Maximum Wavelength for Weights [nm]\n\n".format(inputs['lambdamax_wght'])) f.write("/\n\n") success("Namelist file created: {}\n".format(filename)) def write_geometry(filename, nbi, spec=None, npa=None): """ #+#write_geometry #+Write geometry values to a HDF5 file #+*** #+##Input Arguments #+ **filename**: Name of the geometry file #+ #+ **nbi**: NBI geometry structure #+ #+##Keyword Arguments #+ **spec**: Optional, Spectral geometry structure #+ #+ **npa**: Optional, NPA geometry structure #+ #+##Example Usage #+```python #+>>> write_geometry(filename, nbi, spec=spec, npa=npa) #+``` """ info('Writing geometry file...') # Create and open h5 file with h5py.File(filename, 'w') as hf: # File attributes hf.attrs['description'] = 'Geometric quantities for FIDASIM' # Create nbi group g_nbi = hf.create_group('nbi') # nbi att g_nbi.attrs['description'] = 'Neutral Beam Geometry' g_nbi.attrs['coordinate_system'] = 'Right-handed cartesian' nbi_description = {'data_source': 'Source of the NBI geometry', 'name': 'Beam name', 'src': 'Position of the center of the beam source grid', 'axis':'Axis of the beam centerline: Centerline(t) = src + axis*t ', 'focy': 'Horizonal focal length of the beam', 'focz': 'Vertical focal length of the beam', 'divy': 'Horizonal divergences of the beam. One for each energy component', 'divz': 'Vertical divergences of the beam. One for each energy component', 'widy': 'Half width of the beam source grid', 'widz': 'Half height of the beam source grid', 'shape':'Shape of the beam source grid: 1="rectangular", 2="circular"', 'naperture': 'Number of apertures', 'ashape': 'Shape of the aperture(s): 1="rectangular", 2="circular"', 'awidy': 'Half width of the aperture(s)', 'awidz': 'Half height of the aperture(s)', 'aoffy': 'Horizontal (y) offset of the aperture(s) relative to the +x aligned beam centerline', 'aoffz': 'Vertical (z) offset of the aperture(s) relative to the +x aligned beam centerline', 'adist': 'Distance from the center of the beam source grid to the aperture(s) plane'} nbi_units = {'src': 'cm', 'axis': 'cm', 'focy': 'cm', 'focz': 'cm', 'divy': 'radians', 'divz': 'radians', 'widy': 'cm', 'widz': 'cm', 'awidy': 'cm', 'awidz': 'cm', 'aoffy': 'cm', 'aoffz': 'cm', 'adist': 'cm'} write_data(g_nbi, nbi, desc = nbi_description, units=nbi_units, name='nbi') if spec is not None: # Create spec group g_spec = hf.create_group('spec') # Spectroscopic attributes g_spec.attrs['description'] = 'FIDA/BES Chord Geometry' g_spec.attrs['coordinate_system'] = 'Right-handed cartesian' # Define description attributes spec_description = {'data_source': 'Source of the chord geometry', 'nchan': 'Number of channels', 'system': 'Names of the different spectrocopic systems', 'id': 'Line of sight ID', 'lens': 'Positions of the lenses', 'axis': 'Optical axis of the lines of sight: LOS(t) = lens + axis*t ', 'radius': 'Line of sight radius at midplane or tangency point', 'sigma_pi': 'Ratio of the intensities of the sigma and pi stark lines. Measured quantity', 'spot_size': 'Radius of spot size'} spec_units = {'lens': 'cm', 'axis': 'cm', 'radius': 'cm', 'spot_size': 'cm'} write_data(g_spec, spec, desc=spec_description, units=spec_units, name='spec') if npa is not None: # Create npa group g_npa = hf.create_group('npa') # Group attributes g_npa.attrs['description'] = 'NPA Geometry' g_npa.attrs['coordinate_system'] = 'Right-handed cartesian' # Dataset attributes npa_description = {'data_source': 'Source of the NPA geometry', 'nchan': 'Number of channels', 'system': 'Names of the different NPA systems', 'id': 'Line of sight ID', 'd_shape': 'Shape of the detector: 1="rectangular", 2="circular"', 'd_cent': 'Center of the detector', 'd_tedge': 'Center of the detectors top edge', 'd_redge': 'Center of the detectors right edge', 'a_shape': 'Shape of the aperture: 1="rectangular", 2="circular"', 'a_cent': 'Center of the aperture', 'a_tedge': 'Center of the apertures top edge', 'a_redge': 'Center of the apertures right edge', 'radius': 'Line of sight radius at midplane or tangency point'} npa_units = {'d_cent': 'cm', 'd_tedge': 'cm', 'd_redge': 'cm', 'a_cent': 'cm', 'a_tedge': 'cm', 'radius': 'cm', 'a_redge': 'cm'} write_data(g_npa, npa, desc = npa_description, units = npa_units, name='npa') if os.path.isfile(filename): success('Geometry file created: ' + filename) else: error('Geometry file creation failed.') def write_equilibrium(filename, plasma, fields): """ #+#write_equilibrium #+Write MHD equilibrium values to a HDF5 file #+*** #+##Input Arguments #+ **filename**: Name of the equilibrium file #+ #+ **plasma**: Plasma dictionary #+ #+ **fields**: Electromagnetic fields dictionary #+ #+##Example Usage #+```python #+>>> write_equilibrium(filename, plasma, fields) #+``` """ info('Writing equilibrium file...') with h5py.File(filename, 'w') as hf: # File attribute hf.attrs['description'] = 'Plasma Parameters and Electromagnetic Fields for FIDASIM' # Create plasma group g_plasma = hf.create_group('plasma') # Plasma Attributes g_plasma.attrs['description'] = 'Plasma Parameters' g_plasma.attrs['coordinate_system'] = 'Cylindrical' # Dataset attributes plasma_description = {'data_source': 'Source of the plasma parameters', 'time': 'Time', 'dene': 'Electron Number Density: Dene(r,z)', 'te': 'Electron Temperature: Te(r,z)', 'ti': 'Ion Temperature: Ti(r,z)', 'zeff': 'Effective Nuclear Charge: Zeff(r,z)', 'denn': 'Cold/Edge neutral density: Denn(r,z)', 'vr': 'Bulk plasma flow in the r-direction: Vr(r,z)', 'vt': 'Bulk plasma flow in the theta/torodial-direction: Vt(r,z)', 'vz': 'Bulk plasma flow in the z-direction: Vz(r,z)', 'nr': 'Number of R values', 'nz': 'Number of Z values', 'r': 'Radius', 'z': 'Z', 'r2d': 'Radius grid: R(r,z)', 'z2d': 'Z grid: Z(r,z)', 'mask': 'Boolean mask that indicates where the plasma parameters are well defined'} plasma_units = {'time': 's', 'dene': 'cm^-3', 'denn': 'cm^-3', 'te': 'keV', 'ti': 'keV', 'vr': 'cm/s', 'vt': 'cm/s', 'vz': 'cm/s', 'r': 'cm', 'z': 'cm', 'r2d': 'cm', 'z2d': 'cm'} write_data(g_plasma, plasma, desc = plasma_description, units = plasma_units, name='plasma') # Create fields group g_fields = hf.create_group('fields') # Electromagnetic fields attributes g_fields.attrs['description'] = 'Electromagnetic Fields' g_fields.attrs['coordinate_system'] = 'Cylindrical' fields_description = {'data_source': 'Source of the EM equilibrium', 'mask': 'Boolean mask that indicates where the fields are well defined', 'time': 'Time', 'br': 'Magnetic field in the r-direction: Br(r,z)', 'bt': 'Magnetic field in the theta/torodial-direction: Bt(r,z)', 'bz': 'Magnetic field in the z-direction: Bz(r,z)', 'er': 'Electric field in the r-direction: Er(r,z)', 'et': 'Electric field in the theta/torodial-direction: Et(r,z)', 'ez': 'Electric field in the z-direction: Ez(r,z)', 'nr': 'Number of R values', 'nz': 'Number of Z values', 'r': 'Radius', 'z': 'Z', 'r2d': 'Radius grid: R(r,z)', 'z2d': 'Z grid: Z(r,z)'} fields_units = {'time': 's', 'br': 'T', 'bt': 'T', 'bz': 'T', 'er': 'V/m', 'et': 'V/m', 'ez': 'V/m', 'nr': 'V/m', 'nz': 'V/m', 'r': 'cm', 'z': 'cm', 'r2d': 'cm', 'z2d': 'cm'} write_data(g_fields, fields, desc = fields_description, units = fields_units, name='fields') if os.path.isfile(filename): success('Equilibrium file created: '+filename) else: error('Equilibrium file creation failed.') def write_distribution(filename, distri): """ #+#write_distribution #+Write fast-ion distribution to a HDF5 file #+*** #+##Input Arguments #+ **filename**: Name of the distribution file #+ #+ **dist**: Fast-ion distribution distionary #+ #+##Example Usage #+```dist #+>>> write_distribution(filename, distri) #+``` """ info('Writing fast-ion distribution file...') description = {'data_source': 'Source of the fast-ion distribution', 'type': 'Distribution type: 1="Guiding Center Density Function", 2="Guiding Center ' \ 'Monte Carlo", 3="Full Orbit Monte Carlo"', 'time': 'Distribution time'} units = {'time': 's'} if distri['type'] == 1: description['nenergy'] = 'Number of energy values' description['npitch'] = 'Number of pitch values' description['energy'] = 'Energy' description['pitch'] = 'Pitch: p = v_parallel/v w.r.t. the magnetic field' description['f'] = 'Fast-ion density function: F(E,p,R,Z)' description['denf'] = 'Fast-ion density: Denf(r,z)' description['nr'] = 'Number of R values' description['nz'] = 'Number of Z values' description['r'] = 'Radius' description['z'] = 'Z' description['r2d'] = 'Radius grid: R(r,z)' description['z2d'] = 'Z grid: Z(r,z)' units['energy'] = 'keV' units['f'] = 'fast-ions/(dE*dP*cm^3)' units['denf'] = 'cm^-3' units['r'] = 'cm' units['z'] = 'cm' units['r2d'] = 'cm' units['z2d'] = 'cm' else: description['nparticle'] = 'Number of MC particles' description['nclass'] = 'Number of orbit classes' description['r'] = 'R position of a MC particle' description['z'] = 'Z position of a MC particle' description['weight'] = 'Weight of a MC particle: sum(weight) = # of fast-ions ' description['class'] = 'Orbit class of a MC particle: class in Set(1:nclass)' units['r'] = 'cm' units['z'] = 'cm' units['weight'] = 'fast-ions/particle' if distri['type'] == 2: description['energy'] = 'Energy of a MC particle' description['pitch'] = 'Pitch of a MC particle: p = v_parallel/v w.r.t. the magnetic field' else: description['vr'] ='Radial velocity of a MC particle' description['vt'] = 'Torodial velocity of a MC particle' description['vz'] = 'Z velocity of a MC particle' units['vr'] = 'cm/s' units['vt'] = 'cm/s' units['vz'] = 'cm/s' with h5py.File(filename, 'w') as hf: # File attr hf.attrs['description'] = 'Fast-ion distribution for FIDASIM' hf.attrs['coordinate_system'] = 'Cylindrical' write_data(hf, distri, desc = description, units=units, name='distribution') if os.path.isfile(filename): success('Distribution file created: ' + filename) else: error('Distribution file creation failed.') def prefida(inputs, grid, nbi, plasma, fields, fbm, spec=None, npa=None): """ #+#prefida #+Checks FIDASIM inputs and writes FIDASIM input files #+*** #+##Input Arguments #+ **inputs**: Inputs structure #+ #+ **grid**: Interpolation grid structure #+ #+ **nbi**: Neutral beam geometry structure #+ #+ **plasma**: Plasma parameters structure #+ #+ **fields**: Electromagnetic fields structure #+ #+ **fbm**: Fast-ion distribution structure #+ #+##Keyword Arguments #+ **spec**: Optional, Spectral geometry structure #+ #+ **npa**: Optional, NPA geometry structure #+ #+##Example Usage #+```python #+>>> prefida(inputs, grid, nbi, plasma, fields, fbm, spec=spec, npa=npa) #+``` """ # CHECK INPUTS inputs = check_inputs(inputs) # MAKE DIRECTORIES IF THEY DONT EXIST if not os.path.isdir(inputs['result_dir']): os.makedirs(inputs['result_dir']) # CHECK INTERPOLATION GRID check_grid(grid) # CHECK BEAM INPUTS nbi = check_beam(inputs, nbi) # CHECK PLASMA PARAMETERS plasma = check_plasma(inputs, grid, plasma) # CHECK ELECTROMAGNETIC FIELDS fields = check_fields(inputs, grid, fields) # CHECK FAST-ION DISTRIBUTION fbm = check_distribution(inputs, grid, fbm) # CHECK FIDA/BES if spec is not None: check_spec(inputs, spec) # CHECK NPA if npa is not None: check_npa(inputs, npa) # WRITE FIDASIM INPUT FILES write_namelist(inputs['input_file'], inputs) # WRITE GEOMETRY FILE write_geometry(inputs['geometry_file'], nbi, spec=spec, npa=npa) # WRITE EQUILIBRIUM FILE write_equilibrium(inputs['equilibrium_file'], plasma, fields) # WRITE DISTRIBUTION FILE write_distribution(inputs['distribution_file'], fbm) print('') print('') success('FIDASIM pre-processing completed') print('To run FIDASIM use the following command') print(get_fidasim_dir() + os.sep + 'fidasim ' + inputs['result_dir'] + os.sep + inputs['runid'] + '_inputs.dat') print('') print('')