Changeset 11787


Ignore:
Timestamp:
03/24/12 10:27:17 (13 years ago)
Author:
Eric.Larour
Message:

Create python model and subclasses

Location:
issm/trunk-jpl
Files:
19 added
6 edited

Legend:

Unmodified
Added
Removed

  • issm/trunk-jpl/src/py/README

    r10148 r11787  
    55# launch python
    66
    7 >>> md=mode();
     7>>> md=model();
    88>>> md
    99>>> md.mesh

  • issm/trunk-jpl/src/py/classes/mesh.py

    r10149 r11787  
     1#module imports
     2from fielddisplay import fielddisplay
     3
    14class mesh:
    2         """Python mesh class"""
    3         x = []
    4         y = []
    5         elements = []
    6         def __repr__(self):
    7                 return """x: X coordinates
    8                         y: Y coordinates
    9                                   elements: indexing """
     5        #properties
     6        def __init__(self):
     7                # {{{ Properties
     8                self.x                           = float('NaN');
     9                self.y                           = float('NaN');
     10                self.z                           = float('NaN');
     11                self.elements                    = float('NaN');
     12                self.dimension                   = 0;
     13                self.numberoflayers              = 0;
     14                self.numberofelements            = 0;
     15                self.numberofvertices            = 0;
     16                self.numberofedges               = 0;
     17               
     18                self.lat                         = float('NaN');
     19                self.long                        = float('NaN');
     20                self.hemisphere                  = float('NaN');
     21
     22                self.elementonbed                = float('NaN');
     23                self.elementonsurface            = float('NaN');
     24                self.vertexonbed                 = float('NaN');
     25                self.vertexonsurface             = float('NaN');
     26                self.lowerelements               = float('NaN');
     27                self.lowervertex                 = float('NaN');
     28                self.upperelements               = float('NaN');
     29                self.uppervertex                 = float('NaN');
     30                self.vertexonboundary            = float('NaN');
     31
     32                self.edges                       = float('NaN');
     33                self.segments                    = float('NaN');
     34                self.segmentmarkers              = float('NaN');
     35                self.vertexconnectivity          = float('NaN');
     36                self.elementconnectivity         = float('NaN');
     37                self.average_vertex_connectivity = 0;
     38
     39                self.x2d                         = float('NaN');
     40                self.y2d                         = float('NaN');
     41                self.elements2d                  = float('NaN');
     42                self.numberofvertices2d          = 0;
     43                self.numberofelements2d          = 0;
     44
     45                self.extractedvertices           = float('NaN');
     46                self.extractedelements           = float('NaN');
     47
     48                #}}}
     49        def __repr__(obj):
     50                # {{{ Display
     51
     52                if obj.dimension==3:
     53                        string="\n%s"%("      Elements and vertices of the original 2d mesh:")
     54                       
     55                        string="%s\n%s"%(string,fielddisplay(obj,"numberofelements2d","number of elements"))
     56                        string="%s\n%s"%(string,fielddisplay(obj,"numberofvertices2d","number of vertices"))
     57                        string="%s\n%s"%(string,fielddisplay(obj,"elements2d","index into (x,y,z), coordinates of the vertices"))
     58                        string="%s\n%s"%(string,fielddisplay(obj,"x2d","vertices x coordinate"))
     59                        string="%s\n%s"%(string,fielddisplay(obj,"y2d","vertices y coordinate"))
     60
     61                        string="%s\n%s" %(string,"Elements and vertices of the extruded 3d mesh:")
     62                else:
     63                        string="\n%s"%("      Elements and vertices:")
     64
     65                string="%s\n%s"%(string,fielddisplay(obj,"numberofelements","number of elements"))
     66               
     67
     68
     69
     70                string="%s\n%s"%(string,fielddisplay(obj,"numberofvertices","number of vertices"))
     71                string="%s\n%s"%(string,fielddisplay(obj,"elements","index into (x,y,z), coordinates of the vertices"))
     72                string="%s\n%s"%(string,fielddisplay(obj,"x","vertices x coordinate"))
     73                string="%s\n%s"%(string,fielddisplay(obj,"y","vertices y coordinate"))
     74                string="%s\n%s"%(string,fielddisplay(obj,"z","vertices z coordinate"))
     75                string="%s\n%s"%(string,fielddisplay(obj,"edges","edges of the 2d mesh (vertex1 vertex2 element1 element2)"))
     76                string="%s\n%s"%(string,fielddisplay(obj,"numberofedges","number of edges of the 2d mesh"))
     77
     78                string="%s%s"%(string,"\n      Properties:")
     79               
     80                string="%s\n%s"%(string,fielddisplay(obj,"dimension","mesh dimension (2d or 3d)"))
     81                string="%s\n%s"%(string,fielddisplay(obj,"numberoflayers","number of extrusion layers"))
     82                string="%s\n%s"%(string,fielddisplay(obj,"vertexonbed","lower vertices flags list"))
     83                string="%s\n%s"%(string,fielddisplay(obj,"elementonbed","lower elements flags list"))
     84                string="%s\n%s"%(string,fielddisplay(obj,"vertexonsurface","upper vertices flags list"))
     85                string="%s\n%s"%(string,fielddisplay(obj,"elementonsurface","upper elements flags list"))
     86                string="%s\n%s"%(string,fielddisplay(obj,"uppervertex","upper vertex list (NaN for vertex on the upper surface)"))
     87                string="%s\n%s"%(string,fielddisplay(obj,"upperelements","upper element list (NaN for element on the upper layer)"))
     88                string="%s\n%s"%(string,fielddisplay(obj,"lowervertex","lower vertex list (NaN for vertex on the lower surface)"))
     89                string="%s\n%s"%(string,fielddisplay(obj,"lowerelements","lower element list (NaN for element on the lower layer"))
     90                string="%s\n%s"%(string,fielddisplay(obj,"vertexonboundary","vertices on the boundary of the domain flag list"))
     91               
     92                string="%s\n%s"%(string,fielddisplay(obj,"segments","edges on domain boundary (vertex1 vertex2 element)"))
     93                string="%s\n%s"%(string,fielddisplay(obj,"segmentmarkers","number associated to each segment"))
     94                string="%s\n%s"%(string,fielddisplay(obj,"vertexconnectivity","list of vertices connected to vertex_i"))
     95                string="%s\n%s"%(string,fielddisplay(obj,"elementconnectivity","list of vertices connected to element_i"))
     96                string="%s\n%s"%(string,fielddisplay(obj,"average_vertex_connectivity","average number of vertices connected to one vertex"))
     97
     98                string="%s%s"%(string,"\n      Extracted model:")
     99
     100                string="%s\n%s"%(string,fielddisplay(obj,"extractedvertices","vertices extracted from the model"))
     101                string="%s\n%s"%(string,fielddisplay(obj,"extractedelements","elements extracted from the model"))
     102
     103                string="%s%s"%(string,"\n      Projection:")
     104                string="%s\n%s"%(string,fielddisplay(obj,"lat","vertices latitude"))
     105                string="%s\n%s"%(string,fielddisplay(obj,"long","vertices longitude"))
     106                string="%s\n%s"%(string,fielddisplay(obj,"hemisphere","Indicate hemisphere ""n"" or ""s"" "))
     107                return string
     108                #}}}

  • issm/trunk-jpl/src/py/classes/model.py

    r10148 r11787  
    1 from mesh import *
     1#module imports {{{
     2from mesh import mesh
     3from mask import mask
     4from geometry import geometry
     5from constants import constants
     6from surfaceforcings import surfaceforcings
     7from basalforcings import basalforcings
     8from materials import materials
     9from friction import friction
     10from flowequation import flowequation
     11from timestepping import timestepping
     12from initialization import initialization
     13from rifts import rifts
     14from debug import debug
     15from verbose import verbose
     16from settings import settings
     17from solver import solver
     18#}}}
     19class model:
     20        #properties
     21        def __init__(self):
     22                # {{{ Properties
     23                self.mesh             = mesh()
     24                self.mask             = mask()
     25                self.geometry         = geometry()
     26                self.constants        = constants()
     27                self.surfaceforcings  = surfaceforcings()
     28                self.basalforcings    = basalforcings()
     29                self.materials        = materials()
     30                self.friction         = friction()
     31                self.flowequation     = flowequation()
     32                self.timestepping     = timestepping()
     33                self.initialization   = initialization()
     34                self.rifts            = rifts()
    235
    3 class model:
    4         """Python model class"""
    5         mesh=mesh()
    6         def __init__(self):
    7                 print 'new model created'
    8         def __repr__(self):
    9                 return "   mesh: mesh properties"
     36                self.debug            = debug()
     37                self.verbose          = verbose()
     38                self.settings         = settings()
     39                self.solver           = solver()
     40                self.cluster          = [];
     41
     42                self.balancethickness = [];
     43                self.diagnostic       = [];
     44                self.groundingline    = [];
     45                self.hydrology        = [];
     46                self.prognostic       = [];
     47                self.thermal          = [];
     48                self.steadystate      = [];
     49                self.transient        = [];
     50
     51                self.autodiff         = [];
     52                self.flaim            = [];
     53                self.inversion        = [];
     54                self.qmu              = [];
     55
     56                self.results          = [];
     57                self.radaroverlay     = [];
     58                self.miscellaneous    = [];
     59                self.private          = [];
     60                #}}}
     61        def __repr__(obj):
     62                # {{{ Display
     63
     64                #print "Here %s the number: %d" % ("is", 37)
     65                string="%19s: %-22s -- %s" % ("mesh","[%s,%s]" % ("1x1",obj.mesh.__class__.__name__),"mesh properties")
     66                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("mask","[%s,%s]" % ("1x1",obj.mask.__class__.__name__),"defines grounded and floating elements"))
     67                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("geometry","[%s,%s]" % ("1x1",obj.geometry.__class__.__name__),"surface elevation, bedrock topography, ice thickness,..."))
     68                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("constants","[%s,%s]" % ("1x1",obj.constants.__class__.__name__),"physical constants"))
     69                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("surfaceforcings","[%s,%s]" % ("1x1",obj.surfaceforcings.__class__.__name__),"surface forcings"))
     70                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("basalforcings","[%s,%s]" % ("1x1",obj.basalforcings.__class__.__name__),"bed forcings"))
     71                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("materials","[%s,%s]" % ("1x1",obj.materials.__class__.__name__),"material properties"))
     72                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("friction","[%s,%s]" % ("1x1",obj.friction.__class__.__name__),"basal friction/drag properties"))
     73                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("flowequation","[%s,%s]" % ("1x1",obj.flowequation.__class__.__name__),"flow equations"))
     74                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("timestepping","[%s,%s]" % ("1x1",obj.timestepping.__class__.__name__),"time stepping for transient models"))
     75                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("initialization","[%s,%s]" % ("1x1",obj.initialization.__class__.__name__),"initial guess/state"))
     76                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("rifts","[%s,%s]" % ("1x1",obj.rifts.__class__.__name__),"rifts properties'"))
     77                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("debug","[%s,%s]" % ("1x1",obj.debug.__class__.__name__),"debugging tools (valgrind, gprof"))
     78                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("verbose","[%s,%s]" % ("1x1",obj.verbose.__class__.__name__),"verbosity level in solve"))
     79                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("settings","[%s,%s]" % ("1x1",obj.settings.__class__.__name__),"settings properties"))
     80                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("solver","[%s,%s]" % ("1x1",obj.solver.__class__.__name__),"PETSc options for each solution'"))
     81                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("cluster","[%s,%s]" % ("1x1",obj.cluster.__class__.__name__),"cluster parameters (number of cpus...)"))
     82                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("balancethickness","[%s,%s]" % ("1x1",obj.balancethickness.__class__.__name__),"parameters for balancethickness solution"))
     83                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("diagnostic","[%s,%s]" % ("1x1",obj.diagnostic.__class__.__name__),"parameters for diagnostic solution"))
     84                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("groundingline","[%s,%s]" % ("1x1",obj.groundingline.__class__.__name__),"parameters for groundingline solution"))
     85                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("hydrology","[%s,%s]" % ("1x1",obj.hydrology.__class__.__name__),"parameters for hydrology solution"))
     86                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("prognostic","[%s,%s]" % ("1x1",obj.prognostic.__class__.__name__),"parameters for prognostic solution"))
     87                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("thermal","[%s,%s]" % ("1x1",obj.thermal.__class__.__name__),"parameters for thermal solution"))
     88                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("steadystate","[%s,%s]" % ("1x1",obj.steadystate.__class__.__name__),"parameters for steadystate solution"))
     89                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("transient","[%s,%s]" % ("1x1",obj.transient.__class__.__name__),"parameters for transient solution"))
     90                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("autodiff","[%s,%s]" % ("1x1",obj.autodiff.__class__.__name__),"automatic differentiation parameters"))
     91                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("flaim","[%s,%s]" % ("1x1",obj.flaim.__class__.__name__),"flaim parameters"))
     92                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("inversion","[%s,%s]" % ("1x1",obj.inversion.__class__.__name__),"parameters for inverse methods"))
     93                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("qmu","[%s,%s]" % ("1x1",obj.qmu.__class__.__name__),"dakota properties"))
     94                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("results","[%s,%s]" % ("1x1",obj.results.__class__.__name__),"model results'"))
     95                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("radaroverlay","[%s,%s]" % ("1x1",obj.radaroverlay.__class__.__name__),"radar image for plot overlay"))
     96                string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("miscellaneous","[%s,%s]" % ("1x1",obj.miscellaneous.__class__.__name__),"miscellaneous fields"))
     97                return string;
     98                 #}}}

  • issm/trunk-jpl/src/py/modules/TriMesh/Makefile

    r10148 r11787  
    1 all: ogive
     1all: ice
    22
    33ice:
    44        g++ -bundle  -bind \
    55                -I$(ISSM_TIER)/externalpackages/boost/install/include \
     6                -I/Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m\
    67                -L$(ISSM_TIER)/externalpackages/boost/install/lib -lboost_python \
    7                 -L/usr/lib/python2.6/config/ -lpython2.6 \
     8                -L/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/config-3.2m/ -lpython3.2 \
    89                TriMeshmodule.cpp -o TriMesh.so
    9 
    10 ogive:
    11         g++ \
    12                 -I$(ISSM_TIER)/externalpackages/boost/install/include \
    13                 -I/opt/local/include/python2.5/ \
    14                 -L$(ISSM_TIER)/externalpackages/boost/install/lib -lboost_python \
    15                 -L/usr/lib/ -lpython2.5 \
    16                 TriMeshmodule.cpp -o TriMesh.so -bundle
    1710
    1811clean:

  • issm/trunk-jpl/src/py/modules/hello/Makefile

    r10148 r11787  
    1 all: ogive
     1all: ice
    22
    33ice:
    44        g++ -bundle  -bind \
    55                -I$(ISSM_TIER)/externalpackages/boost/install/include \
    6                 -I/usr/include/python2.6/ \
     6                -I/Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m\
    77                -L$(ISSM_TIER)/externalpackages/boost/install/lib -lboost_python \
    8                 -L/usr/lib/python2.6/config/ -lpython2.6 \
     8                -L/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/config-3.2m/ -lpython3.2 \
    99                hellomodule.cpp -o hello.so
    1010
    11 ogive:
    12         g++ \
    13                 -I$(ISSM_TIER)/externalpackages/boost/install/include \
    14                 -I/usr/include/python2.5/ \
    15                 -L$(ISSM_TIER)/externalpackages/boost/install/lib -lboost_python \
    16                 -L/usr/lib/python2.5/config/ -lpython2.5 \
    17                 hellomodule.cpp -o hello.so -bundle
     11
    1812
    1913clean:

  • issm/trunk-jpl/startup.py

    r10939 r11787  
    1010import os,sys
    1111
     12 
     13#First check we are running python 3 at least
     14if sys.version_info[0] < 3:
     15        print("ISSM can only work in Python 3. Exiting python")
     16        sys.exit(1)
     17
    1218#Recover ISSM_TIER, ISSM_DIR  and USERNAME
    1319ISSM_TIER=os.getenv('ISSM_TIER')
    … …  
    2026#the variable ISSM_TIER in this file, in case it is not correctly setup.
    2127
    22 #ISSM path
    23 sys.path.append(ISSM_TIER+'/src/py')
    24 sys.path.append(ISSM_TIER+'/src/py/classes')
    25 sys.path.append(ISSM_TIER+'/src/py/modules/TriMesh')
    26 sys.path.append(ISSM_TIER+'/src/py/modules/hello')
     28#ISSM path. Go through src/py and load everything we find  that looks like a python file
     29for root,dirs,files in os.walk(ISSM_TIER+ '/src/py'):
     30        for file in files:
     31                if file.find(".py") != -1:
     32                        if file.find(".pyc") == -1:
     33                                #add to path
     34                                sys.path.append(root)
     35                                file=os.path.splitext(file)[0]
     36                                #__import__(file)
     37
     38#Deal with scipy import:
     39import scipy
     40import numpy
     41import nose
     42
     43#Import modules that are absolutely needed in ISSM {{{
    2744from model import *
     45from mesh import *
     46from mask import *
     47from geometry import *
     48from constants import *
     49from surfaceforcings import *
     50from basalforcings import *
     51from materials import *
     52from friction import *
     53from flowequation import *
     54from fielddisplay import *
     55from timestepping import *
     56from initialization import *
     57from rifts import *
     58from debug import *
     59from settings import *
     60from solver import *
     61#}}}
    2862
    29 print "\n  To get started with ISSM, type issmdoc at the command prompt.\n\n"
     63print("\n  To get started with ISSM, type issmdoc at the command prompt.\n\n")
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