1 | import time |
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2 | import math |
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3 | import numpy as np |
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4 | import netCDF4 as cdf |
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5 | import matplotlib.tri as tri |
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6 | import matplotlib.pyplot as plt |
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7 | |
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8 | import dynamico.wrap as wrap |
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9 | from ctypes import c_void_p, c_int, c_double, c_bool |
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10 | radian=180/math.pi |
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11 | |
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12 | #------------- direct Cython interface to DYNAMICO routines -------------# |
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13 | |
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14 | cdef extern from "functions.h": |
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15 | cpdef void init_params() |
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16 | cpdef void setup_xios() |
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17 | cpdef void call_xios_set_timestep(double) |
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18 | cpdef void call_xios_update_calendar(int) |
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19 | |
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20 | #------------- import and wrap DYNAMICO routines -------------# |
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21 | |
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22 | ker=wrap.Struct() # store imported fun X as funs.X |
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23 | |
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24 | check_args = False # use True instead of False for debugging, probably with some overhead |
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25 | |
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26 | try: |
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27 | kernels = wrap.SharedLib(vars(ker), 'libkernels.so', check_args=check_args) |
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28 | setvar, setvars, getvar, getvars = kernels.setvar, kernels.setvars, kernels.getvar, kernels.getvars |
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29 | except OSError: |
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30 | print """ |
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31 | Unable to load shared library 'libkernels.so' ! |
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32 | """ |
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33 | raise |
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34 | |
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35 | # providing a full prototype enables type-checking when calling |
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36 | # if a number n is present in the prototype, the previous type is repeated n times |
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37 | kernels.import_funs([ |
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38 | # ['setup_xios',None], |
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39 | # ['call_xios_set_timestep',c_double], |
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40 | # ['call_xios_update_calendar',c_int] |
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41 | # ['init_params',c_double], |
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42 | ['init_mesh',c_void_p,13], |
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43 | ['init_metric', c_void_p,6], |
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44 | ['init_hybrid', c_void_p,3], |
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45 | ['caldyn_hevi', c_double, c_void_p,20], |
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46 | ['partition_graph', c_int,2, c_void_p,3, c_int, c_void_p], |
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47 | ]) |
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48 | |
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49 | # set/get global variables |
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50 | eta_mass,eta_lag=(1,2) |
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51 | thermo_theta,thermo_entropy,thermo_moist,thermo_boussinesq=(1,2,3,4) |
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52 | |
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53 | kernels.addvars( |
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54 | c_bool,'hydrostatic','debug_hevi_solver','rigid', |
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55 | c_int,'llm','nqdyn','primal_num','max_primal_deg', |
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56 | 'dual_num','max_dual_deg','edge_num','max_trisk_deg', |
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57 | 'caldyn_thermo','caldyn_eta','nb_threads', |
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58 | c_double,'elapsed','g', 'ptop', 'cpp', 'cppv', |
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59 | 'Rd', 'Rv', 'preff', 'Treff', 'pbot', 'rho_bot', 'Phi_bot') |
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60 | |
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61 | elapsed=0. |
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62 | |
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63 | #----------------------------- Base class for dynamics ------------------------ |
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64 | |
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65 | class Caldyn: |
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66 | def __init__(self,mesh): |
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67 | self.mesh=mesh |
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68 | fps, ftheta, fmass = mesh.field_ps, mesh.field_theta, mesh.field_mass |
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69 | fw, fu, fz = mesh.field_w, mesh.field_u, mesh.field_z |
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70 | self.ps, self.ms, self.dms = fps(), fps(), fps() |
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71 | self.s, self.hs, self.dhs = ftheta(), ftheta(), ftheta() |
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72 | self.pk, self.berni, self.geopot, self.hflux = fmass(),fmass(),fw(),fu() |
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73 | self.qu, self.qv = fu(),fz() |
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74 | self.fmass, self.ftheta, self.fu, self.fw = fmass, ftheta, fu, fw |
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75 | def bwd_fast_slow(self, flow, tau): |
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76 | global elapsed |
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77 | time1=time.time() |
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78 | flow,fast,slow = self._bwd_fast_slow_(flow,tau) |
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79 | time2=time.time() |
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80 | elapsed=elapsed+time2-time1 |
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81 | return flow,fast,slow |
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82 | |
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83 | # when calling caldyn_hevi, arrays for tendencies must be re-created each time |
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84 | # to avoid overwriting in the same memory space when time scheme is multi-stage |
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85 | |
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86 | #-------------------------- Shallow-water dynamics --------------------- |
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87 | |
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88 | class Caldyn_RSW(Caldyn): |
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89 | def __init__(self,mesh): |
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90 | Caldyn.__init__(self,mesh) |
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91 | setvars(('hydrostatic','caldyn_thermo','caldyn_eta'), |
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92 | (True,thermo_boussinesq,eta_lag)) |
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93 | self.dhs = self.fmass() |
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94 | ker.init_params() |
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95 | def _bwd_fast_slow_(self, flow, tau): |
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96 | h,u = flow |
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97 | # h*s = h => uniform buoyancy s=1 => shallow-water |
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98 | dh, du_slow, du_fast, hs, buf = self.fmass(), self.fu(), self.fu(), h.copy(), self.geopot |
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99 | ker.caldyn_hevi(tau, self.ms, h, hs, u, self.geopot, buf, |
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100 | self.s, self.ps, self.pk, self.hflux, self.qv, |
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101 | self.dms, dh, self.dhs, du_fast, du_slow, |
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102 | buf, buf, buf, buf) |
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103 | return (h,u), (0.,du_fast), (dh,du_slow) |
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104 | |
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105 | #----------------------------------- HPE ------------------------------------ |
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106 | |
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107 | class Caldyn_HPE(Caldyn): |
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108 | def __init__(self,caldyn_thermo,caldyn_eta, mesh,metric,thermo,BC,g): |
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109 | Caldyn.__init__(self,mesh) |
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110 | setvars(('hydrostatic','caldyn_thermo','caldyn_eta', |
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111 | 'g','ptop','Rd','cpp','preff','Treff'), |
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112 | (True,caldyn_thermo,caldyn_eta, |
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113 | g,BC.ptop,thermo.Rd,thermo.Cpd,thermo.p0,thermo.T0)) |
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114 | ker.init_params() |
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115 | def _bwd_fast_slow_(self, flow, tau): |
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116 | dm, dS, du_slow, du_fast, buf = self.fmass(), self.ftheta(), self.fu(), self.fu(), self.geopot |
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117 | m,S,u = flow |
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118 | ker.caldyn_hevi(tau, self.ms, m, S, u, self.geopot, buf, |
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119 | self.s, self.ps, self.pk, self.hflux, self.qv, |
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120 | self.dms, dm, dS, du_fast, du_slow, |
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121 | buf, buf, buf, buf) |
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122 | return (m,S,u), (0.,0.,du_fast), (dm,dS,du_slow) |
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123 | |
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124 | #----------------------------------- NH ------------------------------------ |
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125 | |
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126 | class Caldyn_NH(Caldyn): |
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127 | def __init__(self,caldyn_thermo,caldyn_eta, mesh,metric,thermo,BC,g): |
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128 | Caldyn.__init__(self,mesh) |
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129 | setvars(('hydrostatic','caldyn_thermo','caldyn_eta', |
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130 | 'g','ptop','Rd','cpp','preff','Treff', |
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131 | 'pbot','rho_bot'), |
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132 | (False,caldyn_thermo,caldyn_eta, |
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133 | g,BC.ptop,thermo.Rd,thermo.Cpd,thermo.p0,thermo.T0, |
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134 | BC.pbot.max(), BC.rho_bot.max())) |
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135 | ker.init_params() |
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136 | def bwd_fast_slow(self, flow, tau): |
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137 | ftheta, fmass, fu, fw = self.ftheta, self.fmass, self.fu, self.fw |
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138 | dm, dS, du_slow, du_fast = fmass(), ftheta(), fu(), fu() |
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139 | dPhi_slow, dPhi_fast, dW_slow, dW_fast = fw(), fw(), fw(), fw() |
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140 | m,S,u,Phi,W = flow |
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141 | ker.caldyn_hevi(tau, self.ms, m, S, u, Phi, W, |
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142 | self.s, self.ps, self.pk, self.hflux, self.qv, |
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143 | self.dms, dm, dS, du_fast, du_slow, |
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144 | dPhi_fast, dPhi_slow, dW_fast, dW_slow) |
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145 | return ((m,S,u,Phi,W), (0.,0.,du_fast,dPhi_fast,dW_fast), |
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146 | (dm,dS,du_slow,dPhi_slow,dW_slow)) |
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147 | |
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148 | #-------------------------------- Hybrid mass-based coordinate ------------- |
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149 | |
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150 | # compute hybrid coefs from distribution of mass |
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151 | def compute_hybrid_coefs(mass): |
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152 | nx,llm=mass.shape |
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153 | mass_dak = np.zeros((nx,llm)) |
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154 | mass_dbk = np.zeros((nx,llm)) |
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155 | mass_bl = np.zeros((nx,llm+1))+1. |
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156 | for i in range(nx): |
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157 | m_i = mass[i,:] |
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158 | dbk_i = m_i/sum(m_i) |
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159 | mass_dbk[i,:] = dbk_i |
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160 | mass_bl[i,1:]= 1.-dbk_i.cumsum() |
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161 | return mass_bl, mass_dak, mass_dbk |
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162 | |
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163 | #----------------------- Cartesian mesh ----------------------- |
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164 | |
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165 | def squeeze(dims): |
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166 | # return np.zeros(dims) |
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167 | return np.zeros([n for n in dims if n>1]) |
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168 | |
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169 | # arrays is a list of arrays |
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170 | # vals is a list of tuples |
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171 | # each tuple is stored in each array |
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172 | def put(ij, deg, arrays, vals): |
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173 | k=0 |
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174 | for vv in vals: # vv is a tuple of values to be stored in arrays |
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175 | for array,v in zip(arrays,vv): |
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176 | array[ij,k]=v |
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177 | k=k+1 |
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178 | deg[ij]=k |
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179 | |
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180 | class Cartesian_mesh: |
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181 | def __init__(self,nx,ny,llm,nqdyn,Lx,Ly,f): |
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182 | dx,dy = Lx/nx, Ly/ny |
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183 | self.dx, self.dy, self.f = dx,dy,f |
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184 | self.nx, self.ny, self.llm, self.nqdyn = nx,ny,llm,nqdyn |
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185 | self.field_z = self.field_mass |
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186 | # 1D coordinate arrays |
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187 | x=(np.arange(nx)-nx/2.)*Lx/nx |
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188 | y=(np.arange(ny)-ny/2.)*Ly/ny |
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189 | lev=np.arange(llm) |
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190 | levp1=np.arange(llm+1) |
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191 | self.x, self.y, self.lev, self.levp1 = x,y,lev,levp1 |
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192 | # 3D coordinate arrays |
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193 | self.xx,self.yy,self.ll = np.meshgrid(x,y,lev, indexing='ij') |
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194 | self.xxp1,self.yyp1,self.llp1 = np.meshgrid(x,y,levp1, indexing='ij') |
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195 | # beware conventions for indexing |
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196 | # Fortran order : llm,nx*ny,nqdyn / indices start at 1 |
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197 | # Python order : nqdyn,ny,nx,llm / indices start at 0 |
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198 | # indices below follow Fortran while x,y follow Python/C |
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199 | index=lambda x,y : ((x+(nx*(y+2*ny)))%(nx*ny))+1 |
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200 | indexu=lambda x,y : 2*index(x,y)-1 |
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201 | indexv=lambda x,y : 2*index(x,y) |
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202 | indices = lambda shape : np.zeros(shape,np.int32) |
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203 | |
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204 | primal_nb = indices(nx*ny) |
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205 | primal_edge = indices((nx*ny,4)) |
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206 | primal_ne = indices((nx*ny,4)) |
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207 | |
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208 | dual_nb = indices(nx*ny) |
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209 | dual_edge = indices((nx*ny,4)) |
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210 | dual_ne = indices((nx*ny,4)) |
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211 | dual_vertex = indices((nx*ny,4)) |
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212 | Riv2 = np.zeros((nx*ny,4)) |
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213 | |
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214 | left = indices(2*nx*ny) |
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215 | right = indices(2*nx*ny) |
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216 | up = indices(2*nx*ny) |
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217 | down = indices(2*nx*ny) |
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218 | le_de = np.zeros(2*nx*ny) |
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219 | |
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220 | trisk_deg = indices(2*nx*ny) |
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221 | trisk = indices((2*nx*ny,4)) # 4 TRiSK coefs per edge |
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222 | wee = np.zeros((2*nx*ny,4)) |
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223 | |
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224 | for x in range(nx): |
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225 | for y in range(ny): |
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226 | # NB : Fortran indices start at 1 |
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227 | # primal cells |
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228 | put(index(x,y)-1,primal_nb,(primal_edge,primal_ne), |
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229 | ((indexu(x,y),1), |
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230 | (indexv(x,y),1), |
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231 | (indexu(x-1,y),-1), |
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232 | (indexv(x,y-1),-1) )) |
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233 | # dual cells |
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234 | put(index(x,y)-1,dual_nb,(dual_edge,dual_vertex,dual_ne,Riv2), |
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235 | ((indexv(x+1,y),index(x,y),1,.25), |
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236 | (indexu(x,y+1),index(x+1,y),-1,.25), |
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237 | (indexv(x,y),index(x+1,y+1),-1,.25), |
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238 | (indexu(x,y),index(x,y+1),1,.25) )) |
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239 | # edges : |
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240 | # left and right are adjacent primal cells |
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241 | # flux is positive when going from left to right |
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242 | # up and down are adjacent dual cells (vertices) |
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243 | # circulation is positive when going from down to up |
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244 | # u-points |
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245 | ij =indexu(x,y)-1 |
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246 | left[ij]=index(x,y) |
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247 | right[ij]=index(x+1,y) |
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248 | down[ij]=index(x,y-1) |
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249 | up[ij]=index(x,y) |
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250 | le_de[ij]=dy/dx |
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251 | put(ij,trisk_deg,(trisk,wee),( |
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252 | (indexv(x,y),-.25), |
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253 | (indexv(x+1,y),-.25), |
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254 | (indexv(x,y-1),-.25), |
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255 | (indexv(x+1,y-1),-.25))) |
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256 | # v-points |
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257 | ij = indexv(x,y)-1 |
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258 | left[ij]=index(x,y) |
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259 | right[ij]=index(x,y+1) |
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260 | down[ij]=index(x,y) |
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261 | up[ij]=index(x-1,y) |
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262 | le_de[ij]=dx/dy |
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263 | put(ij,trisk_deg,(trisk,wee),( |
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264 | (indexu(x,y),.25), |
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265 | (indexu(x-1,y),.25), |
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266 | (indexu(x,y+1),.25), |
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267 | (indexu(x-1,y+1),.25))) |
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268 | setvars(('llm','nqdyn','edge_num','primal_num','dual_num', |
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269 | 'max_trisk_deg','max_primal_deg','max_dual_deg'), |
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270 | (llm,nqdyn,2*nx*ny,nx*ny,nx*ny,4,4,4) ) |
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271 | ker.init_mesh(primal_nb,primal_edge,primal_ne, |
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272 | dual_nb,dual_edge,dual_ne,dual_vertex, |
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273 | left,right,down,up,trisk_deg,trisk) |
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274 | |
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275 | Aiv=np.zeros(nx*ny)+dx*dy # Ai=Av=dx*dy |
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276 | ker.init_metric(Aiv,Aiv,f+0.*Aiv,le_de,Riv2,-wee) |
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277 | def field_theta(self): return squeeze((self.nqdyn,self.ny,self.nx,self.llm)) |
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278 | def field_mass(self): return squeeze((self.ny,self.nx,self.llm)) |
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279 | def field_z(self): return squeeze((self.ny,self.nx,self.llm)) |
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280 | def field_w(self): return squeeze((self.ny,self.nx,self.llm+1)) |
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281 | def field_u(self): return np.zeros((self.ny,2*self.nx,self.llm)) |
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282 | def field_ps(self): return squeeze((self.ny,self.nx)) |
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283 | def ucomp(self,u): return u[:,range(0,2*self.nx,2),:] |
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284 | def set_ucomp(self,uv,u): uv[:,range(0,2*self.nx,2),:]=u |
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285 | def vcomp(self,u): return u[:,range(1,2*self.nx,2),:] |
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286 | |
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287 | #---------------------- MPAS fully unstructured mesh ------------------------ |
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288 | |
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289 | def compute_ne(num,deg,edges,left,right): |
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290 | ne = np.zeros_like(edges) |
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291 | for cell in range(num): |
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292 | for iedge in range(deg[cell]): |
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293 | edge = edges[cell,iedge]-1 |
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294 | if left[edge]==cell+1: ne[cell,iedge]+=1 |
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295 | if right[edge]==cell+1: ne[cell,iedge]-=1 |
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296 | if ne[cell,iedge]==0 : print 'error at cell,iedge', cell, iedge |
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297 | return ne |
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298 | |
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299 | def plot(tri,data): |
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300 | plt.figure(figsize=(12,4)) |
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301 | plt.gca().set_aspect('equal') |
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302 | plt.tricontourf(tri, data, 20) |
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303 | plt.colorbar() |
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304 | plt.ylim((-90,90)) |
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305 | plt.xlim((0,360)) |
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306 | |
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307 | class MPAS_Mesh: |
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308 | def __init__(self, gridfile, llm, nqdyn, radius, f): |
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309 | self.gridfile, self.llm, self.nqdyn = gridfile,llm,nqdyn |
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310 | self.radius, self.f = radius, f |
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311 | # open mesh file, get main dimensions |
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312 | try: |
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313 | nc = cdf.Dataset(gridfile, "r") |
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314 | except RuntimeError: |
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315 | print """ |
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316 | Unable to open grid file %s, maybe you forgot to download it ? |
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317 | To do so, go to the 'Python/' dir and execute './get_MPAS_grids.sh'. |
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318 | """ % gridfile |
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319 | raise |
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320 | |
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321 | def getdims(*names): return [len(nc.dimensions[name]) for name in names] |
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322 | def getvars(*names): |
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323 | for name in names : print "getvar %s ..."%name |
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324 | time1=time.time() |
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325 | ret=[nc.variables[name][:] for name in names] |
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326 | print "... Done in %f seconds"%(time.time()-time1) |
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327 | return ret |
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328 | primal_num, edge_num, dual_num = getdims('nCells','nEdges','nVertices') |
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329 | print 'Number of primal cells, dual cells and edges : %d, %d, %d '%(primal_num,dual_num,edge_num) |
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330 | primal_deg, trisk_deg = getvars('nEdgesOnCell','nEdgesOnEdge') |
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331 | dual_deg = [3 for i in range(dual_num) ] |
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332 | dual_deg = np.ascontiguousarray(dual_deg,dtype=np.int32) # NB : Fortran code expects 32-bit ints |
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333 | |
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334 | # get indices for stencils |
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335 | # primal -> vertices (unused) |
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336 | primal_vertex, dual_vertex = getvars('verticesOnCell','cellsOnVertex') |
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337 | # primal <-> edges |
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338 | primal_edge, left_right = getvars('edgesOnCell','cellsOnEdge') |
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339 | left,right = left_right[:,0], left_right[:,1] |
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340 | primal_ne = compute_ne(primal_num,primal_deg,primal_edge,left,right) |
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341 | # dual <-> edges |
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342 | dual_edge, down_up = getvars('edgesOnVertex','verticesOnEdge') |
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343 | down,up = down_up[:,0], down_up[:,1] |
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344 | dual_ne = compute_ne(dual_num,dual_deg,dual_edge,up,down) |
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345 | # primal <-> dual, edges <-> edges (TRiSK) |
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346 | dual_vertex, trisk = getvars('cellsOnVertex','edgesOnEdge') |
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347 | # get positions, lengths, surfaces and weights |
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348 | le,de,Ai,Av = getvars('dvEdge','dcEdge','areaCell','areaTriangle') |
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349 | lat_i,lon_i = getvars('latCell','lonCell') |
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350 | lat_v,lon_v = getvars('latVertex','lonVertex') |
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351 | lat_e,lon_e,angle_e = getvars('latEdge','lonEdge','angleEdge') |
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352 | wee,Riv2 = getvars('weightsOnEdge','kiteAreasOnVertex') |
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353 | |
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354 | # fix normalization of wee and Riv2 weights |
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355 | for edge1 in range(edge_num): |
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356 | for i in range(trisk_deg[edge1]): |
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357 | edge2=trisk[edge1,i]-1 # NB Fortran vs C/Python indexing |
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358 | wee[edge1,i] = de[edge1]*wee[edge1,i]/le[edge2] |
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359 | for ivertex in range(dual_num): |
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360 | for j in range(3): |
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361 | Riv2[ivertex,j]=Riv2[ivertex,j]/Av[ivertex] |
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362 | r=Riv2[ivertex,:] |
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363 | r=sum(r) |
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364 | if abs(r-1.)>1e-6 : print 'error with Riv2 at vertex ', ivertex |
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365 | |
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366 | max_primal_deg, max_dual_deg, max_trisk_deg = getdims('maxEdges','vertexDegree','maxEdges2') |
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367 | |
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368 | # CRITICAL : force arrays left, etc. to be contiguous in memory: |
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369 | left,right,up,down = [np.ascontiguousarray(x) for x in (left,right,up,down)] |
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370 | trisk,wee,primal_edge = [np.ascontiguousarray(x) for x in (trisk,wee,primal_edge)] |
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371 | |
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372 | print ('Max stencil sizes (div,curl,trisk) : %d, %d, %d' |
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373 | % (max_primal_deg, max_dual_deg, max_trisk_deg) ) |
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374 | |
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375 | r2 = radius**2 |
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376 | Av = r2*Av |
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377 | fv = f(lon_v,lat_v) # Coriolis parameter |
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378 | self.Ai, self.Av, self.fv = r2*Ai,Av,fv |
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379 | self.le, self.de, self.le_de = radius*le, radius*de, le/de |
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380 | self.trisk_deg, self.trisk, self.wee = trisk_deg, trisk, wee |
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381 | setvars(('llm','nqdyn','edge_num','primal_num','dual_num', |
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382 | 'max_trisk_deg','max_primal_deg','max_dual_deg'), |
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383 | (llm, nqdyn, edge_num, primal_num,dual_num, |
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384 | max_trisk_deg, max_primal_deg, max_dual_deg) ) |
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385 | |
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386 | ker.init_mesh(primal_deg,primal_edge,primal_ne, |
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387 | dual_deg,dual_edge,dual_ne,dual_vertex, |
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388 | left,right,down,up,trisk_deg,trisk) |
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389 | ker.init_metric(self.Ai,self.Av,self.fv,le/de,Riv2,wee) |
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390 | |
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391 | for edge in range(edge_num): |
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392 | iedge = trisk[edge,0:trisk_deg[edge]] |
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393 | if iedge.min()<1 : |
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394 | print 'error' |
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395 | |
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396 | self.primal_num, self.edge_num, self.dual_num = primal_num, edge_num, dual_num |
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397 | def period(x) : return (x+2*math.pi)%(2*math.pi) |
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398 | lon_i, lon_v, lon_e = map(period, (lon_i,lon_v,lon_e)) |
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399 | self.lon_i, self.lat_i = lon_i, lat_i |
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400 | self.lon_v, self.lat_v = lon_v, lat_v |
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401 | self.lon_e, self.lat_e, self.angle_e = lon_e, lat_e, angle_e |
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402 | self.primal_deg, self.primal_vertex = primal_deg, primal_vertex |
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403 | self.primal = tri.Triangulation(lon_i*180./math.pi, lat_i*180./math.pi) |
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404 | self.dual_deg, self.dual_vertex = dual_deg, dual_vertex |
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405 | self.dual = tri.Triangulation(lon_v*180./math.pi, lat_v*180./math.pi) |
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406 | self.triedge = tri.Triangulation(lon_e*180./math.pi, lat_e*180./math.pi) |
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407 | self.dx = de.min() |
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408 | self.lon3D_i, self.ll3D = np.meshgrid(lon_i, range(llm)) |
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409 | self.lat3D_i, self.ll3D = np.meshgrid(lat_i, range(llm)) |
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410 | def field_theta(self): return squeeze((self.nqdyn,self.primal_num,self.llm)) |
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411 | def field_mass(self): return squeeze((self.primal_num,self.llm)) |
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412 | def field_z(self): return squeeze((self.dual_num,self.llm)) |
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413 | def field_w(self): return squeeze((self.primal_num,self.llm+1)) |
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414 | def field_u(self): return squeeze((self.edge_num,self.llm)) |
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415 | def field_ps(self): return squeeze((self.primal_num,)) |
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416 | def ucov2D(self, ulon, ulat): |
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417 | return self.de*(ulon*np.cos(self.angle_e)+ulat*np.sin(self.angle_e)) |
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418 | def ucov3D(self, ulon, ulat): |
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419 | ucov = np.zeros((self.edge_num,ulon.shape[1])) |
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420 | for edge in range(self.edge_num): |
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421 | angle=self.angle_e[edge] |
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422 | ucov[edge,:] = self.de[edge]*(ulon[edge,:]*math.cos(angle)+ulat[edge,:]*math.sin(angle)) |
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423 | return ucov |
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424 | def plot_i(self,data): |
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425 | plot(self.primal,data) |
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426 | def plot_v(self,data): |
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427 | plot(self.dual,data) |
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428 | def plot_e(self,data): |
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429 | plot(self.triedge,data) |
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430 | |
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431 | #-------------------------------------- Mesh partitioning ------------------------------------------# |
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432 | |
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433 | # Helper functions and interface to ParMETIS |
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434 | # list_stencil converts an adjacency graph from array format index[num_cells, MAX_EDGES] to compressed format |
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435 | # loc_stencil returns the start/end indices (vtxdist) expected by ParMETIS |
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436 | # i.e. index[start:end] with start=vtxdist[cell], end=vtxdist[cell+1] lists the edges of cell 'cell' |
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437 | |
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438 | def list_stencil(degree, stencil, cond=lambda x:True): |
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439 | for i in range(degree.size): |
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440 | for j in range(degree[i]): |
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441 | s=stencil[i,j] |
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442 | if cond(s): yield stencil[i,j] |
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443 | |
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444 | def loc_stencil(degree, stencil): |
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445 | loc=0 |
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446 | for i in range(degree.size): |
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447 | yield loc |
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448 | loc=loc+degree[i] |
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449 | yield loc |
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450 | |
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451 | def partition_mesh(degree, stencil, nparts): |
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452 | # arguments : PArray1D and PArray2D describing mesh, number of desired partitions |
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453 | dim_cell, degree, stencil = degree.dim, degree.data, stencil.data |
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454 | comm, vtxdist, idx_start, idx_end = dim_cell.comm, dim_cell.vtxdist, dim_cell.start, dim_cell.end |
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455 | mpi_rank, mpi_size = comm.Get_rank(), comm.Get_size() |
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456 | adjncy_loc, xadj_loc = list_stencil(degree, stencil), loc_stencil(degree, stencil) |
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457 | adjncy_loc, xadj_loc = [np.asarray(list(x), dtype=np.int32) for x in (adjncy_loc, xadj_loc)] |
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458 | owner = np.zeros(idx_end-idx_start, dtype=np.int32); |
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459 | ker.partition_graph(mpi_rank, mpi_size, vtxdist, xadj_loc, adjncy_loc, nparts, owner) |
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460 | return owner |
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461 | |
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462 | def partition_from_stencil(owner2, degree, stencil): |
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463 | # given a stencil dim1->dim2 and owner2 on dim2, define owner[i] on dim1 as min(stencil[i,:] if i is even, max if odd |
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464 | dim1, dim2= degree.dim, owner2.dim |
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465 | degree, stencil, n = degree.data, stencil.data, dim1.end-dim1.start |
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466 | cells2 = list_stencil(degree, stencil) |
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467 | cells2 = sorted(list(set(list(cells2)))) # list of cells for which we need to know owner2 |
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468 | get2 = dim2.getter(cells2) |
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469 | owner1, owner2, glob2loc = np.zeros(n, dtype=np.int32), get2(owner2), get2.dict |
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470 | for i in range(n): |
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471 | owners = [ owner2[glob2loc[stencil[i,j]]] for j in range(degree[i]) ] |
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472 | if i%2 == 0 : owner1[i] = min(owners) |
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473 | else : owner1[i] = max(owners) |
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474 | return owner1 |
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475 | |
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476 | def find_my_cells(owner): # a PArray1D containing the data returned by partition_mesh |
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477 | dim, comm, owner = owner.dim, owner.dim.comm, owner.data |
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478 | mpi_rank, mpi_size = comm.Get_rank(), comm.Get_size() |
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479 | cells=[set() for i in range(mpi_size)] |
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480 | for i in range(len(owner)): |
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481 | cells[owner[i]].add(dim.start+i) |
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482 | cells = [sorted(list(cells[i])) for i in range(mpi_size)] |
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483 | mycells = comm.alltoall(cells) |
---|
484 | mycells = sorted(sum(mycells, [])) # concatenate into a single list |
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485 | return mycells |
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486 | |
---|
487 | #---------------------------------- Stencil management ---------------------------------------# |
---|
488 | |
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489 | # Class Stencil represents an adjacency relationship (e.g. cell=>edges) |
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490 | # using adjacency information read from PArrays |
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491 | # It computes a list of "edges" adjacent to a given list of "cells" |
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492 | # This is used to form the sets E0 -> C0 -> E1 -> V1 -> E2 -> C1 |
---|
493 | # which are then used to form lists of global indices for V1,C1,E2 such that |
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494 | # C0, E0, E1 form contiguous subsets of C1, E2 starting from 0 |
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495 | |
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496 | def reindex(vertex_dict, degree, bounds): |
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497 | for i in range(degree.size): |
---|
498 | for j in range(degree[i]): |
---|
499 | bounds[i,j] = vertex_dict[bounds[i,j]] |
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500 | |
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501 | class Stencil_glob: |
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502 | def __init__(self, degree, neigh, weight=None): |
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503 | self.degree, self.neigh, self.weight = degree, neigh, weight |
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504 | def __call__(self, cells, neigh_dict=None): |
---|
505 | return Stencil(cells, self.degree, self.neigh, neigh_dict, self.weight) |
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506 | |
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507 | class Stencil: |
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508 | def __init__(self, cells, degree, neigh, neigh_dict, weight=None): |
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509 | get = degree.dim.getter(cells) |
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510 | mydegree, myneigh = [get(x) for x in (degree, neigh)] |
---|
511 | if not weight is None : myweight = get(weight) |
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512 | if neigh_dict is None : |
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513 | keep = lambda n : True |
---|
514 | else : # if neigh_dict is present, only neighbours in dict are retained |
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515 | keep = lambda n : n in neigh_dict |
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516 | neigh_set = list_stencil(mydegree, myneigh, keep) |
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517 | self.neigh_set = list(set(list(neigh_set) )) |
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518 | rej=0 |
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519 | for i in range(len(mydegree)): # keep only elements in neigh_dict, in-place |
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520 | k=0 |
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521 | for j in range(mydegree[i]): |
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522 | n=myneigh[i,j] |
---|
523 | if keep(n): |
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524 | myneigh[i,k]=n |
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525 | if not weight is None : myweight[i,k]=myweight[i,j] |
---|
526 | k=k+1 |
---|
527 | else: |
---|
528 | rej=rej+1 |
---|
529 | mydegree[i]=k |
---|
530 | if neigh_dict is None: |
---|
531 | neigh_dict = {j:i for i,j in enumerate(self.neigh_set)} |
---|
532 | myneigh_loc = reindex(neigh_dict, mydegree, myneigh) |
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533 | self.degree, self.neigh_glob, self.neigh_loc = mydegree, myneigh, myneigh_loc |
---|
534 | |
---|
535 | def progressive_iter(mylist, cell_lists): |
---|
536 | for thelist in cell_lists: |
---|
537 | mylist = mylist + list(set(thelist)-set(mylist)) |
---|
538 | yield mylist |
---|
539 | def progressive_list(*cell_lists): |
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540 | # cell_lists : a tuple of lists of global indices, with each list a subset of the next |
---|
541 | # returns : a list 'mylist' such that for each list 'thelist' in cell_lists, thelist = mylist[0:len(thelist)] |
---|
542 | # example : edge_list = progressive_list(E0,E1,E2) with E0,E1,E2 increasing lists of cell edges |
---|
543 | return list(progressive_iter([], cell_lists)) |
---|
544 | |
---|