Tests IO BPCH

import and go into GEOS-Chem rundirs directory


In [1]:
from pygchem.io import bpch
import numpy as np

In [2]:
#%cd /home/data/GEOS-Chem/GEOS-Chem-rundirs/
%cd /home/benbovy/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/


/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs

4x5 GEOS5 Standard CTM


In [3]:
%cd 4x5/geos5/standard/
ctm_filename = 'ctm.bpch'


/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos5/standard

In [4]:
%timeit bpch.read_bpch(ctm_filename)


1 loops, best of 3: 167 ms per loop

In [5]:
%timeit bpch.read_bpch(ctm_filename, skip_data=False)


1 loops, best of 3: 3.75 s per loop

In [6]:
filetype, title, datablocks = bpch.read_bpch(ctm_filename)

In [7]:
filetype


Out[7]:
'CTM bin 02'

In [8]:
title


Out[8]:
'GEOS-CHEM binary punch file v. 2.0'

In [9]:
print len(datablocks)
datablocks[0]


285
Out[9]:
{'category': 'DUSTSRCE',
 'center180': True,
 'data': <BPCHDataProxy shape=(72, 46) dtype='f' path='/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos5/standard/ctm.bpch' file_position=356 scale_factor=1.0>,
 'diaginfo': {'description': 'Dust emission',
  'name': 'DUSTSRCE',
  'offset': 4000},
 'file_position': 356,
 'halfpolar': True,
 'loaded_from_file': '/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos5/standard/ctm.bpch',
 'modelname': 'GEOS5_47L',
 'name': 'DST1',
 'number': 38,
 'origin': (1, 1, 1),
 'resolution': (5.0, 4.0),
 'save_to_file': '',
 'shape': (72, 46),
 'times': (datetime.datetime(2005, 7, 1, 0, 0),
  datetime.datetime(2005, 8, 1, 0, 0)),
 'tracerinfo': {'carbon_weight': 1,
  'chemical': True,
  'full_name': 'DST1 tracer',
  'hydrocarbon': False,
  'molecular_weight': 0.029,
  'name': 'DST1',
  'number': 4038,
  'scale': 1.0,
  'unit': 'kg'},
 'unit': 'kg'}

In [10]:
dust_source = datablocks[0]
dust_source['data'].data


Out[10]:
array([[ 0.,  0.,  0., ...,  0.,  0.,  0.],
       [ 0.,  0.,  0., ...,  0.,  0.,  0.],
       [ 0.,  0.,  0., ...,  0.,  0.,  0.],
       ..., 
       [ 0.,  0.,  0., ...,  0.,  0.,  0.],
       [ 0.,  0.,  0., ...,  0.,  0.,  0.],
       [ 0.,  0.,  0., ...,  0.,  0.,  0.]])

In [11]:
%timeit bpch.write_bpch('ctm_test.bpch', datablocks, title, filetype)


1 loops, best of 3: 8.29 s per loop

In [12]:
import hashlib

def hashfile(afile, hasher, blocksize=65536):
    buf = afile.read(blocksize)
    while len(buf) > 0:
        hasher.update(buf)
        buf = afile.read(blocksize)
    return hasher.hexdigest()

h1 = hashfile(open('ctm.bpch', 'rb'), hashlib.sha256())
h2 = hashfile(open('ctm_test.bpch', 'rb'), hashlib.sha256())
print h1
print h2


6b333cc9fa074280962c4c52cc33d015fd125ca72c1e9082188011f9fdbd4a9f
8bf0453ced5b917b164d21cd8300555186117699ec2854286b0760e6561f9d5c

In [13]:
!ls -all


total 225505
drwx------ 1 benbovy users      850 Aug  5 20:09 .
drwx------ 1 benbovy users      204 Feb  3  2014 ..
-rw------- 1 benbovy users      610 Feb  3  2014 chemga.dat
-rw------- 1 benbovy users 87475420 Feb  3  2014 ctm.bpch
-rw-r--r-- 1 benbovy users 87475420 Aug  7 20:29 ctm_test.bpch
-rw------- 1 benbovy users    11110 Feb  3  2014 diaginfo.dat
-rw------- 1 benbovy users     6148 Feb  3  2014 .DS_Store
drwx------ 1 benbovy users      408 Feb  3  2014 .git
-rw------- 1 benbovy users   154237 Feb  3  2014 globchem.dat
-rw------- 1 benbovy users    88064 Feb  3  2014 globchem.db
-rw------- 1 benbovy users    14197 Feb  3  2014 input.geos
-rw------- 1 benbovy users   117454 Feb  3  2014 jv_atms.dat
-rw------- 1 benbovy users     6600 Feb  3  2014 jv_spec_aod.dat
-rw------- 1 benbovy users    33257 Feb  3  2014 jv_spec.dat
-rw------- 1 benbovy users      905 Feb  3  2014 mglob.dat
-rw-r--r-- 1 benbovy users   623020 Feb  3  2014 new_ctm.bpch
-rw------- 1 benbovy users   623020 Feb  3  2014 Ox.mass.final
-rw------- 1 benbovy users   623020 Feb  3  2014 Ox.mass.initial
-rw------- 1 benbovy users     7522 Feb  3  2014 ratj.d
-rw------- 1 benbovy users      351 Feb  3  2014 README
-rw------- 1 benbovy users 26784148 Feb  3  2014 restart.4x5.geos5.2005070100
-rw------- 1 benbovy users 26784148 Feb  3  2014 restart.4x5.geos5.2005080100
-rw------- 1 benbovy users    44607 Feb  3  2014 smv2.log
-rw------- 1 benbovy users    36716 Feb  3  2014 tracerinfo.dat
drwx------ 1 benbovy users      340 Feb  3  2014 vtk

In [14]:
filetype2, title2, datablocks2 = bpch.read_bpch('ctm_test.bpch')

In [15]:
all([np.all(d1['data'].data == d2['data'].data) for d1, d2 in zip(datablocks, datablocks2)])


Out[15]:
True

In [16]:
all([d1['times'] == d2['times']for d1, d2 in zip(datablocks, datablocks2)])


Out[16]:
True

In [17]:
n_air = datablocks[-1]
n_air


Out[17]:
{'category': 'BXHGHT-$',
 'center180': True,
 'data': <BPCHDataProxy shape=(72, 46, 47) dtype='f' path='/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos5/standard/ctm.bpch' file_position=86852756 scale_factor=1.0>,
 'diaginfo': {'description': 'Boxheight, airmass, etc',
  'name': 'BXHGHT-$',
  'offset': 24000},
 'file_position': 86852756,
 'halfpolar': True,
 'loaded_from_file': '/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos5/standard/ctm.bpch',
 'modelname': 'GEOS5_47L',
 'name': 'N(AIR)',
 'number': 4,
 'origin': (1, 1, 1),
 'resolution': (5.0, 4.0),
 'save_to_file': '',
 'shape': (72, 46, 47),
 'times': (datetime.datetime(2005, 7, 1, 0, 0),
  datetime.datetime(2005, 8, 1, 0, 0)),
 'tracerinfo': {'carbon_weight': 1,
  'chemical': False,
  'full_name': 'Number density of air',
  'hydrocarbon': False,
  'molecular_weight': 0.0,
  'name': 'N(AIR)',
  'number': 24004,
  'scale': 1.0,
  'unit': 'molec/m3'},
 'unit': 'molec/m3'}

In [18]:
tes = np.arange(10*5*1).reshape((10,5,1))
tes2 = tes.flatten('F')
tes2.reshape((10,5), order='F') == tes.reshape((10,5))


Out[18]:
array([[ True,  True,  True,  True,  True],
       [ True,  True,  True,  True,  True],
       [ True,  True,  True,  True,  True],
       [ True,  True,  True,  True,  True],
       [ True,  True,  True,  True,  True],
       [ True,  True,  True,  True,  True],
       [ True,  True,  True,  True,  True],
       [ True,  True,  True,  True,  True],
       [ True,  True,  True,  True,  True],
       [ True,  True,  True,  True,  True]], dtype=bool)

In [19]:
datablocks[193]


Out[19]:
{'category': 'IJ-AVG-$',
 'center180': True,
 'data': <BPCHDataProxy shape=(72, 46, 47) dtype='f' path='/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos5/standard/ctm.bpch' file_position=53447048 scale_factor=1000000000.0>,
 'diaginfo': {'description': 'Tracer concentration',
  'name': 'IJ-AVG-$',
  'offset': 0},
 'file_position': 53447048,
 'halfpolar': True,
 'loaded_from_file': '/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos5/standard/ctm.bpch',
 'modelname': 'GEOS5_47L',
 'name': 'Ox',
 'number': 2,
 'origin': (1, 1, 1),
 'resolution': (5.0, 4.0),
 'save_to_file': '',
 'shape': (72, 46, 47),
 'times': (datetime.datetime(2005, 7, 1, 0, 0),
  datetime.datetime(2005, 8, 1, 0, 0)),
 'tracerinfo': {'carbon_weight': 1,
  'chemical': True,
  'full_name': 'Ox tracer',
  'hydrocarbon': False,
  'molecular_weight': 0.048,
  'name': 'Ox',
  'number': 2,
  'scale': 1000000000.0,
  'unit': 'ppbv'},
 'unit': 'ppbv'}

GEOS4 Standard Restart


In [20]:
%cd -
%cd 4x5/geos4/standard/
ctm_filename = 'restart.4x5.geos4.2005070100'


/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs
/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos4/standard

In [21]:
filetype, title, datablocks = bpch.read_bpch(ctm_filename)

In [22]:
print filetype
print title


CTM bin 02
CTM output saved by GAMAP 01/14/2014 10:48

In [23]:
datablocks


Out[23]:
[{'category': 'IJ-AVG-$',
  'center180': True,
  'data': <BPCHDataProxy shape=(72, 46, 30) dtype='f' path='/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos4/standard/restart.4x5.geos4.2005070100' file_position=356 scale_factor=1000000000.0>,
  'diaginfo': {'description': 'Tracer concentration',
   'name': 'IJ-AVG-$',
   'offset': 0},
  'file_position': 356,
  'halfpolar': True,
  'loaded_from_file': '/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos4/standard/restart.4x5.geos4.2005070100',
  'modelname': 'GEOS4_30L',
  'name': 'NO',
  'number': 1,
  'origin': (1, 1, 1),
  'resolution': (5.0, 4.0),
  'save_to_file': '',
  'shape': (72, 46, 30),
  'times': (datetime.datetime(2005, 7, 1, 0, 0),
   datetime.datetime(2005, 7, 1, 0, 0)),
  'tracerinfo': {'carbon_weight': 1,
   'chemical': True,
   'full_name': 'NO tracer',
   'hydrocarbon': False,
   'molecular_weight': 0.03,
   'name': 'NO',
   'number': 1,
   'scale': 1000000000.0,
   'unit': 'ppbv'},
  'unit': 'v/v'},
 {'category': 'IJ-AVG-$',
  'center180': True,
  'data': <BPCHDataProxy shape=(72, 46, 30) dtype='f' path='/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos4/standard/restart.4x5.geos4.2005070100' file_position=398024 scale_factor=1000000000.0>,
  'diaginfo': {'description': 'Tracer concentration',
   'name': 'IJ-AVG-$',
   'offset': 0},
  'file_position': 398024,
  'halfpolar': True,
  'loaded_from_file': '/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos4/standard/restart.4x5.geos4.2005070100',
  'modelname': 'GEOS4_30L',
  'name': 'O3',
  'number': 2,
  'origin': (1, 1, 1),
  'resolution': (5.0, 4.0),
  'save_to_file': '',
  'shape': (72, 46, 30),
  'times': (datetime.datetime(2005, 7, 1, 0, 0),
   datetime.datetime(2005, 7, 1, 0, 0)),
  'tracerinfo': {'carbon_weight': 1,
   'chemical': True,
   'full_name': 'O3 tracer',
   'hydrocarbon': False,
   'molecular_weight': 0.048,
   'name': 'O3',
   'number': 2,
   'scale': 1000000000.0,
   'unit': 'ppbv'},
  'unit': 'v/v'},
 {'category': 'IJ-AVG-$',
  'center180': True,
  'data': <BPCHDataProxy shape=(72, 46, 30) dtype='f' path='/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos4/standard/restart.4x5.geos4.2005070100' file_position=795692 scale_factor=1000000000.0>,
  'diaginfo': {'description': 'Tracer concentration',
   'name': 'IJ-AVG-$',
   'offset': 0},
  'file_position': 795692,
  'halfpolar': True,
  'loaded_from_file': '/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos4/standard/restart.4x5.geos4.2005070100',
  'modelname': 'GEOS4_30L',
  'name': 'PAN',
  'number': 3,
  'origin': (1, 1, 1),
  'resolution': (5.0, 4.0),
  'save_to_file': '',
  'shape': (72, 46, 30),
  'times': (datetime.datetime(2005, 7, 1, 0, 0),
   datetime.datetime(2005, 7, 1, 0, 0)),
  'tracerinfo': {'carbon_weight': 1,
   'chemical': True,
   'full_name': 'PAN tracer',
   'hydrocarbon': False,
   'molecular_weight': 0.121,
   'name': 'PAN',
   'number': 3,
   'scale': 1000000000.0,
   'unit': 'ppbv'},
  'unit': 'v/v'},
 {'category': 'IJ-AVG-$',
  'center180': True,
  'data': <BPCHDataProxy shape=(72, 46, 30) dtype='f' path='/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos4/standard/restart.4x5.geos4.2005070100' file_position=1193360 scale_factor=1000000000.0>,
  'diaginfo': {'description': 'Tracer concentration',
   'name': 'IJ-AVG-$',
   'offset': 0},
  'file_position': 1193360,
  'halfpolar': True,
  'loaded_from_file': '/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos4/standard/restart.4x5.geos4.2005070100',
  'modelname': 'GEOS4_30L',
  'name': 'CO',
  'number': 4,
  'origin': (1, 1, 1),
  'resolution': (5.0, 4.0),
  'save_to_file': '',
  'shape': (72, 46, 30),
  'times': (datetime.datetime(2005, 7, 1, 0, 0),
   datetime.datetime(2005, 7, 1, 0, 0)),
  'tracerinfo': {'carbon_weight': 1,
   'chemical': True,
   'full_name': 'CO tracer',
   'hydrocarbon': False,
   'molecular_weight': 0.028,
   'name': 'CO',
   'number': 4,
   'scale': 1000000000.0,
   'unit': 'ppbv'},
  'unit': 'v/v'},
 {'category': 'IJ-AVG-$',
  'center180': True,
  'data': <BPCHDataProxy shape=(72, 46, 30) dtype='f' path='/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos4/standard/restart.4x5.geos4.2005070100' file_position=1591028 scale_factor=1000000000.0>,
  'diaginfo': {'description': 'Tracer concentration',
   'name': 'IJ-AVG-$',
   'offset': 0},
  'file_position': 1591028,
  'halfpolar': True,
  'loaded_from_file': '/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos4/standard/restart.4x5.geos4.2005070100',
  'modelname': 'GEOS4_30L',
  'name': 'ALK4',
  'number': 5,
  'origin': (1, 1, 1),
  'resolution': (5.0, 4.0),
  'save_to_file': '',
  'shape': (72, 46, 30),
  'times': (datetime.datetime(2005, 7, 1, 0, 0),
   datetime.datetime(2005, 7, 1, 0, 0)),
  'tracerinfo': {'carbon_weight': 4,
   'chemical': True,
   'full_name': 'ALK4 tracer',
   'hydrocarbon': True,
   'molecular_weight': 0.012,
   'name': 'ALK4',
   'number': 5,
   'scale': 1000000000.0,
   'unit': 'ppbC'},
  'unit': 'v/v'},
 {'category': 'IJ-AVG-$',
  'center180': True,
  'data': <BPCHDataProxy shape=(72, 46, 30) dtype='f' path='/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos4/standard/restart.4x5.geos4.2005070100' file_position=1988696 scale_factor=1000000000.0>,
  'diaginfo': {'description': 'Tracer concentration',
   'name': 'IJ-AVG-$',
   'offset': 0},
  'file_position': 1988696,
  'halfpolar': True,
  'loaded_from_file': '/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos4/standard/restart.4x5.geos4.2005070100',
  'modelname': 'GEOS4_30L',
  'name': 'ISOP',
  'number': 6,
  'origin': (1, 1, 1),
  'resolution': (5.0, 4.0),
  'save_to_file': '',
  'shape': (72, 46, 30),
  'times': (datetime.datetime(2005, 7, 1, 0, 0),
   datetime.datetime(2005, 7, 1, 0, 0)),
  'tracerinfo': {'carbon_weight': 5,
   'chemical': True,
   'full_name': 'ISOP tracer',
   'hydrocarbon': True,
   'molecular_weight': 0.012,
   'name': 'ISOP',
   'number': 6,
   'scale': 1000000000.0,
   'unit': 'ppbC'},
  'unit': 'v/v'},
 {'category': 'IJ-AVG-$',
  'center180': True,
  'data': <BPCHDataProxy shape=(72, 46, 30) dtype='f' path='/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos4/standard/restart.4x5.geos4.2005070100' file_position=2386364 scale_factor=1000000000.0>,
  'diaginfo': {'description': 'Tracer concentration',
   'name': 'IJ-AVG-$',
   'offset': 0},
  'file_position': 2386364,
  'halfpolar': True,
  'loaded_from_file': '/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos4/standard/restart.4x5.geos4.2005070100',
  'modelname': 'GEOS4_30L',
  'name': 'HNO3',
  'number': 7,
  'origin': (1, 1, 1),
  'resolution': (5.0, 4.0),
  'save_to_file': '',
  'shape': (72, 46, 30),
  'times': (datetime.datetime(2005, 7, 1, 0, 0),
   datetime.datetime(2005, 7, 1, 0, 0)),
  'tracerinfo': {'carbon_weight': 1,
   'chemical': True,
   'full_name': 'HNO3 tracer',
   'hydrocarbon': False,
   'molecular_weight': 0.063,
   'name': 'HNO3',
   'number': 7,
   'scale': 1000000000.0,
   'unit': 'ppbv'},
  'unit': 'v/v'},
 {'category': 'IJ-AVG-$',
  'center180': True,
  'data': <BPCHDataProxy shape=(72, 46, 30) dtype='f' path='/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos4/standard/restart.4x5.geos4.2005070100' file_position=2784032 scale_factor=1000000000.0>,
  'diaginfo': {'description': 'Tracer concentration',
   'name': 'IJ-AVG-$',
   'offset': 0},
  'file_position': 2784032,
  'halfpolar': True,
  'loaded_from_file': '/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos4/standard/restart.4x5.geos4.2005070100',
  'modelname': 'GEOS4_30L',
  'name': 'H2O2',
  'number': 8,
  'origin': (1, 1, 1),
  'resolution': (5.0, 4.0),
  'save_to_file': '',
  'shape': (72, 46, 30),
  'times': (datetime.datetime(2005, 7, 1, 0, 0),
   datetime.datetime(2005, 7, 1, 0, 0)),
  'tracerinfo': {'carbon_weight': 1,
   'chemical': True,
   'full_name': 'H2O2 tracer',
   'hydrocarbon': False,
   'molecular_weight': 0.034,
   'name': 'H2O2',
   'number': 8,
   'scale': 1000000000.0,
   'unit': 'ppbv'},
  'unit': 'v/v'},
 {'category': 'IJ-AVG-$',
  'center180': True,
  'data': <BPCHDataProxy shape=(72, 46, 30) dtype='f' path='/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos4/standard/restart.4x5.geos4.2005070100' file_position=3181700 scale_factor=1000000000.0>,
  'diaginfo': {'description': 'Tracer concentration',
   'name': 'IJ-AVG-$',
   'offset': 0},
  'file_position': 3181700,
  'halfpolar': True,
  'loaded_from_file': '/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos4/standard/restart.4x5.geos4.2005070100',
  'modelname': 'GEOS4_30L',
  'name': 'ACET',
  'number': 9,
  'origin': (1, 1, 1),
  'resolution': (5.0, 4.0),
  'save_to_file': '',
  'shape': (72, 46, 30),
  'times': (datetime.datetime(2005, 7, 1, 0, 0),
   datetime.datetime(2005, 7, 1, 0, 0)),
  'tracerinfo': {'carbon_weight': 3,
   'chemical': True,
   'full_name': 'ACET tracer',
   'hydrocarbon': True,
   'molecular_weight': 0.012,
   'name': 'ACET',
   'number': 9,
   'scale': 1000000000.0,
   'unit': 'ppbC'},
  'unit': 'v/v'},
 {'category': 'IJ-AVG-$',
  'center180': True,
  'data': <BPCHDataProxy shape=(72, 46, 30) dtype='f' path='/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos4/standard/restart.4x5.geos4.2005070100' file_position=3579368 scale_factor=1000000000.0>,
  'diaginfo': {'description': 'Tracer concentration',
   'name': 'IJ-AVG-$',
   'offset': 0},
  'file_position': 3579368,
  'halfpolar': True,
  'loaded_from_file': '/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos4/standard/restart.4x5.geos4.2005070100',
  'modelname': 'GEOS4_30L',
  'name': 'MEK',
  'number': 10,
  'origin': (1, 1, 1),
  'resolution': (5.0, 4.0),
  'save_to_file': '',
  'shape': (72, 46, 30),
  'times': (datetime.datetime(2005, 7, 1, 0, 0),
   datetime.datetime(2005, 7, 1, 0, 0)),
  'tracerinfo': {'carbon_weight': 4,
   'chemical': True,
   'full_name': 'MEK tracer',
   'hydrocarbon': True,
   'molecular_weight': 0.012,
   'name': 'MEK',
   'number': 10,
   'scale': 1000000000.0,
   'unit': 'ppbC'},
  'unit': 'v/v'},
 {'category': 'IJ-AVG-$',
  'center180': True,
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   'hydrocarbon': False,
   'molecular_weight': 0.118,
   'name': 'IEPOX',
   'number': 62,
   'scale': 1000000000.0,
   'unit': 'ppbv'},
  'unit': 'v/v'},
 {'category': 'IJ-AVG-$',
  'center180': True,
  'data': <BPCHDataProxy shape=(72, 46, 30) dtype='f' path='/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos4/standard/restart.4x5.geos4.2005070100' file_position=24655772 scale_factor=1000000000.0>,
  'diaginfo': {'description': 'Tracer concentration',
   'name': 'IJ-AVG-$',
   'offset': 0},
  'file_position': 24655772,
  'halfpolar': True,
  'loaded_from_file': '/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos4/standard/restart.4x5.geos4.2005070100',
  'modelname': 'GEOS4_30L',
  'name': 'MAP',
  'number': 63,
  'origin': (1, 1, 1),
  'resolution': (5.0, 4.0),
  'save_to_file': '',
  'shape': (72, 46, 30),
  'times': (datetime.datetime(2005, 7, 1, 0, 0),
   datetime.datetime(2005, 7, 1, 0, 0)),
  'tracerinfo': {'carbon_weight': 1,
   'chemical': True,
   'full_name': 'MAP tracer',
   'hydrocarbon': False,
   'molecular_weight': 0.076,
   'name': 'MAP',
   'number': 63,
   'scale': 1000000000.0,
   'unit': 'ppbv'},
  'unit': 'v/v'},
 {'category': 'IJ-AVG-$',
  'center180': True,
  'data': <BPCHDataProxy shape=(72, 46, 30) dtype='f' path='/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos4/standard/restart.4x5.geos4.2005070100' file_position=25053440 scale_factor=1000000000.0>,
  'diaginfo': {'description': 'Tracer concentration',
   'name': 'IJ-AVG-$',
   'offset': 0},
  'file_position': 25053440,
  'halfpolar': True,
  'loaded_from_file': '/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos4/standard/restart.4x5.geos4.2005070100',
  'modelname': 'GEOS4_30L',
  'name': 'NO2',
  'number': 64,
  'origin': (1, 1, 1),
  'resolution': (5.0, 4.0),
  'save_to_file': '',
  'shape': (72, 46, 30),
  'times': (datetime.datetime(2005, 7, 1, 0, 0),
   datetime.datetime(2005, 7, 1, 0, 0)),
  'tracerinfo': {'carbon_weight': 1,
   'chemical': True,
   'full_name': 'NO2 tracer',
   'hydrocarbon': False,
   'molecular_weight': 0.046,
   'name': 'NO2',
   'number': 64,
   'scale': 1000000000.0,
   'unit': 'ppbv'},
  'unit': 'v/v'},
 {'category': 'IJ-AVG-$',
  'center180': True,
  'data': <BPCHDataProxy shape=(72, 46, 30) dtype='f' path='/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos4/standard/restart.4x5.geos4.2005070100' file_position=25451108 scale_factor=1000000000.0>,
  'diaginfo': {'description': 'Tracer concentration',
   'name': 'IJ-AVG-$',
   'offset': 0},
  'file_position': 25451108,
  'halfpolar': True,
  'loaded_from_file': '/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos4/standard/restart.4x5.geos4.2005070100',
  'modelname': 'GEOS4_30L',
  'name': 'NO3',
  'number': 65,
  'origin': (1, 1, 1),
  'resolution': (5.0, 4.0),
  'save_to_file': '',
  'shape': (72, 46, 30),
  'times': (datetime.datetime(2005, 7, 1, 0, 0),
   datetime.datetime(2005, 7, 1, 0, 0)),
  'tracerinfo': {'carbon_weight': 1,
   'chemical': True,
   'full_name': 'NO3 tracer',
   'hydrocarbon': False,
   'molecular_weight': 0.062,
   'name': 'NO3',
   'number': 65,
   'scale': 1000000000.0,
   'unit': 'ppbv'},
  'unit': 'v/v'},
 {'category': 'IJ-AVG-$',
  'center180': True,
  'data': <BPCHDataProxy shape=(72, 46, 30) dtype='f' path='/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos4/standard/restart.4x5.geos4.2005070100' file_position=25848776 scale_factor=1000000000.0>,
  'diaginfo': {'description': 'Tracer concentration',
   'name': 'IJ-AVG-$',
   'offset': 0},
  'file_position': 25848776,
  'halfpolar': True,
  'loaded_from_file': '/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/4x5/geos4/standard/restart.4x5.geos4.2005070100',
  'modelname': 'GEOS4_30L',
  'name': 'HNO2',
  'number': 66,
  'origin': (1, 1, 1),
  'resolution': (5.0, 4.0),
  'save_to_file': '',
  'shape': (72, 46, 30),
  'times': (datetime.datetime(2005, 7, 1, 0, 0),
   datetime.datetime(2005, 7, 1, 0, 0)),
  'tracerinfo': {'carbon_weight': 1,
   'chemical': True,
   'full_name': 'HNO2 tracer',
   'hydrocarbon': False,
   'molecular_weight': 0.047,
   'name': 'HNO2',
   'number': 66,
   'scale': 1000000000.0,
   'unit': 'ppbv'},
  'unit': 'v/v'}]

1mo benchmark v9-02r-geosfp


In [24]:
%cd -
%cd 1mo_benchmarks/v9-02/v9-02r.geosfp/


/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs
/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/1mo_benchmarks/v9-02/v9-02r.geosfp

In [25]:
ctm_filename = 'ctm.bpch.v9-02r.geosfp'
filetype, title, datablocks = bpch.read_bpch(ctm_filename)

In [26]:
print filetype
print title


CTM bin 02
GEOS-CHEM binary punch file v. 2.0

In [27]:
print len(datablocks)
print datablocks[-1]


406
{'category': 'DXYP', 'origin': (1, 1, 1), 'save_to_file': '', 'modelname': 'GEOSFP_47L', 'name': 'DXYP', 'halfpolar': True, 'center180': True, 'number': 1, 'data': <BPCHDataProxy shape=(72, 46) dtype='f' path='/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/1mo_benchmarks/v9-02/v9-02r.geosfp/ctm.bpch.v9-02r.geosfp' file_position=117496472 scale_factor=1.0>, 'times': (datetime.datetime(2013, 7, 1, 0, 0), datetime.datetime(2013, 8, 1, 0, 0)), 'shape': (72, 46), 'loaded_from_file': '/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/1mo_benchmarks/v9-02/v9-02r.geosfp/ctm.bpch.v9-02r.geosfp', 'file_position': 117496472, 'diaginfo': {'description': 'Surface area', 'name': 'DXYP', 'offset': 25000}, 'tracerinfo': {'scale': 1.0, 'name': 'DXYP', 'number': 25001, 'molecular_weight': 0.0, 'chemical': False, 'hydrocarbon': False, 'full_name': 'Grid box surface area', 'carbon_weight': 1, 'unit': 'm2'}, 'resolution': (5.0, 4.0), 'unit': 'm2'}

In [28]:
datablocks[-1]['data'].data


Out[28]:
array([[  2.16047078e+09,   1.72679762e+10,   3.44518246e+10, ...,
          3.44518246e+10,   1.72679762e+10,   2.16047078e+09],
       [  2.16047078e+09,   1.72679762e+10,   3.44518246e+10, ...,
          3.44518246e+10,   1.72679762e+10,   2.16047078e+09],
       [  2.16047078e+09,   1.72679762e+10,   3.44518246e+10, ...,
          3.44518246e+10,   1.72679762e+10,   2.16047078e+09],
       ..., 
       [  2.16047078e+09,   1.72679762e+10,   3.44518246e+10, ...,
          3.44518246e+10,   1.72679762e+10,   2.16047078e+09],
       [  2.16047078e+09,   1.72679762e+10,   3.44518246e+10, ...,
          3.44518246e+10,   1.72679762e+10,   2.16047078e+09],
       [  2.16047078e+09,   1.72679762e+10,   3.44518246e+10, ...,
          3.44518246e+10,   1.72679762e+10,   2.16047078e+09]])

1mo benchmark v9-02o_SOA


In [29]:
%cd -
%cd 1mo_benchmarks/v9-02/v9-02o_SOA/


/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs
/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/1mo_benchmarks/v9-02/v9-02o_SOA

In [30]:
ctm_filename = 'ctm.bpch.v9-02o_SOA'
filetype, title, datablocks = bpch.read_bpch(ctm_filename)

In [31]:
print filetype
print title


CTM bin 02
GEOS-CHEM binary punch file v. 2.0

In [32]:
print len(datablocks)
print datablocks[-1]


482
{'category': 'DXYP', 'origin': (1, 1, 1), 'save_to_file': '', 'modelname': 'GEOS5_47L', 'name': 'DXYP', 'halfpolar': True, 'center180': True, 'number': 1, 'data': <BPCHDataProxy shape=(72, 46) dtype='f' path='/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/1mo_benchmarks/v9-02/v9-02o_SOA/ctm.bpch.v9-02o_SOA' file_position=180680264 scale_factor=1.0>, 'times': (datetime.datetime(2005, 7, 1, 0, 0), datetime.datetime(2005, 8, 1, 0, 0)), 'shape': (72, 46), 'loaded_from_file': '/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/1mo_benchmarks/v9-02/v9-02o_SOA/ctm.bpch.v9-02o_SOA', 'file_position': 180680264, 'diaginfo': {'description': 'Surface area', 'name': 'DXYP', 'offset': 25000}, 'tracerinfo': {'scale': 1.0, 'name': 'DXYP', 'number': 25001, 'molecular_weight': 0.0, 'chemical': False, 'hydrocarbon': False, 'full_name': 'Grid box surface area', 'carbon_weight': 1, 'unit': 'm2'}, 'resolution': (5.0, 4.0), 'unit': 'm2'}

In [33]:
datablocks[-1]['data'].data


Out[33]:
array([[  2.16047078e+09,   1.72679762e+10,   3.44518246e+10, ...,
          3.44518246e+10,   1.72679762e+10,   2.16047078e+09],
       [  2.16047078e+09,   1.72679762e+10,   3.44518246e+10, ...,
          3.44518246e+10,   1.72679762e+10,   2.16047078e+09],
       [  2.16047078e+09,   1.72679762e+10,   3.44518246e+10, ...,
          3.44518246e+10,   1.72679762e+10,   2.16047078e+09],
       ..., 
       [  2.16047078e+09,   1.72679762e+10,   3.44518246e+10, ...,
          3.44518246e+10,   1.72679762e+10,   2.16047078e+09],
       [  2.16047078e+09,   1.72679762e+10,   3.44518246e+10, ...,
          3.44518246e+10,   1.72679762e+10,   2.16047078e+09],
       [  2.16047078e+09,   1.72679762e+10,   3.44518246e+10, ...,
          3.44518246e+10,   1.72679762e+10,   2.16047078e+09]])

ND49 Diagnostic (3D-subset timeseries)


In [34]:
%cd -
%cd ND49_example


/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs
/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/ND49_example

In [35]:
ctm_filename = 'ts.joch.200401010300.bpch'
filetype, title, datablocks = bpch.read_bpch(ctm_filename)

In [36]:
print filetype
print title


CTM bin 02
GEOS-CHEM DIAG49 instantaneous timeseries

In [37]:
datablocks[0]


Out[37]:
{'category': 'IJ-AVG-$',
 'center180': True,
 'data': <BPCHDataProxy shape=(2, 2, 47) dtype='f' path='/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/ND49_example/ts.joch.200401010300.bpch' file_position=356 scale_factor=1000000000.0>,
 'diaginfo': {'description': 'Tracer concentration',
  'name': 'IJ-AVG-$',
  'offset': 0},
 'file_position': 356,
 'halfpolar': True,
 'loaded_from_file': '/mnt/hgfs/Aldebaran/ScientificResearch/geoschem/GEOS-Chem-rundirs/ND49_example/ts.joch.200401010300.bpch',
 'modelname': 'GEOS5_47L',
 'name': 'PAN',
 'number': 3,
 'origin': (76, 69, 1),
 'resolution': (2.5, 2.0),
 'save_to_file': '',
 'shape': (2, 2, 47),
 'times': (datetime.datetime(2004, 1, 1, 3, 0),
  datetime.datetime(2004, 1, 1, 3, 0)),
 'tracerinfo': {'carbon_weight': 1,
  'chemical': True,
  'full_name': 'PAN tracer',
  'hydrocarbon': False,
  'molecular_weight': 0.121,
  'name': 'PAN',
  'number': 3,
  'scale': 1000000000.0,
  'unit': 'ppbv'},
 'unit': 'ppbv'}

In [37]: