Index: /issm/trunk-jpl/src/py/README =================================================================== --- /issm/trunk-jpl/src/py/README (revision 11786) +++ /issm/trunk-jpl/src/py/README (revision 11787) @@ -5,5 +5,5 @@ # launch python ->>> md=mode(); +>>> md=model(); >>> md >>> md.mesh Index: /issm/trunk-jpl/src/py/classes/basalforcings.py =================================================================== --- /issm/trunk-jpl/src/py/classes/basalforcings.py (revision 11787) +++ /issm/trunk-jpl/src/py/classes/basalforcings.py (revision 11787) @@ -0,0 +1,20 @@ +#module imports +from fielddisplay import fielddisplay + +class basalforcings: + #properties + def __init__(self): + # {{{ Properties + self.melting_rate = float('NaN') + self.melting_rate_correction = float('NaN') + self.geothermalflux = float('NaN') + #}}} + def __repr__(obj): + # {{{ Display + string=" basal forcings parameters:" + + string="%s\n\n%s"%(string,fielddisplay(obj,"melting_rate","basal melting rate (positive if melting)")) + string="%s\n%s"%(string,fielddisplay(obj,"melting_rate_correction","additional melting applied when the grounding line retreats")) + string="%s\n%s"%(string,fielddisplay(obj,"geothermalflux","geothermal heat flux [W/m^2]")) + return string + #}}} Index: /issm/trunk-jpl/src/py/classes/constants.py =================================================================== --- /issm/trunk-jpl/src/py/classes/constants.py (revision 11787) +++ /issm/trunk-jpl/src/py/classes/constants.py (revision 11787) @@ -0,0 +1,21 @@ +#module imports +from fielddisplay import fielddisplay + +class constants: + #properties + def __init__(self): + # {{{ Properties + self.g = 0 + self.yts = 0 + self.referencetemperature = 0 + #}}} + def __repr__(obj): + # {{{ Display + string=" constants parameters:" + string="%s\n\n%s"%(string,fielddisplay(obj,"g","gravitational acceleration")) + string="%s\n%s"%(string,fielddisplay(obj,"yts","number of seconds in a year")) + string="%s\n%s"%(string,fielddisplay(obj,"referencetemperature","reference temperature used in the enthalpy model")) + + + return string + #}}} Index: /issm/trunk-jpl/src/py/classes/debug.py =================================================================== --- /issm/trunk-jpl/src/py/classes/debug.py (revision 11787) +++ /issm/trunk-jpl/src/py/classes/debug.py (revision 11787) @@ -0,0 +1,18 @@ +#module imports +from fielddisplay import fielddisplay + +class debug: + #properties + def __init__(self): + # {{{ Properties + self.valgrind=False + self.gprof = False + #}}} + def __repr__(obj): + # {{{ Display + string=" debug parameters:" + + string="%s\n\n%s"%(string,fielddisplay(obj,"valgrind","use Valgrind to debug (0 or 1)")) + string="%s\n%s"%(string,fielddisplay(obj,"gprof","use gnu-profiler to find out where the time is spent")) + return string + #}}} Index: /issm/trunk-jpl/src/py/classes/flowequation.py =================================================================== --- /issm/trunk-jpl/src/py/classes/flowequation.py (revision 11787) +++ /issm/trunk-jpl/src/py/classes/flowequation.py (revision 11787) @@ -0,0 +1,31 @@ +#module imports +from fielddisplay import fielddisplay + +class flowequation: + #properties + def __init__(self): + # {{{ Properties + + self.ismacayealpattyn = 0; + self.ishutter = 0; + self.isstokes = 0; + self.vertex_equation = float('NaN') + self.element_equation = float('NaN') + self.bordermacayeal = float('NaN') + self.borderpattyn = float('NaN') + self.borderstokes = float('NaN') + #}}} + def __repr__(obj): + # {{{ Display + string=' flow equation parameters:' + + string="%s\n\n%s"%(string,fielddisplay(obj,'ismacayealpattyn','is the macayeal or pattyn approximation used ?')) + string="%s\n%s"%(string,fielddisplay(obj,'ishutter','is the shallow ice approximation used ?')) + string="%s\n%s"%(string,fielddisplay(obj,'isstokes','are the Full-Stokes equations used ?')) + string="%s\n%s"%(string,fielddisplay(obj,'vertex_equation','flow equation for each vertex')) + string="%s\n%s"%(string,fielddisplay(obj,'element_equation','flow equation for each element')) + string="%s\n%s"%(string,fielddisplay(obj,'bordermacayeal','vertices on MacAyeal''s border (for tiling)')) + string="%s\n%s"%(string,fielddisplay(obj,'borderpattyn','vertices on Pattyn''s border (for tiling)')) + string="%s\n%s"%(string,fielddisplay(obj,'borderstokes','vertices on Stokes'' border (for tiling)')) + return string + #}}} Index: /issm/trunk-jpl/src/py/classes/friction.py =================================================================== --- /issm/trunk-jpl/src/py/classes/friction.py (revision 11787) +++ /issm/trunk-jpl/src/py/classes/friction.py (revision 11787) @@ -0,0 +1,19 @@ +#module imports +from fielddisplay import fielddisplay + +class friction: + #properties + def __init__(self): + # {{{ Properties + self.coefficient = float('NaN') + self.p = float('NaN') + self.q = float('NaN') + #}}} + def __repr__(obj): + # {{{ Display + string="Sigma= drag^2 * Neff ^r * u ^s, with Neff=rho_ice*g*thickness+rho_water*g*bed, r=q/p and s=1/p" + string="%s\n\n%s"%(string,fielddisplay(obj,"coefficient","friction coefficient [SI]")) + string="%s\n%s"%(string,fielddisplay(obj,"p","p exponent")) + string="%s\n%s"%(string,fielddisplay(obj,"q","q exponent")) + return string + #}}} Index: /issm/trunk-jpl/src/py/classes/geometry.py =================================================================== --- /issm/trunk-jpl/src/py/classes/geometry.py (revision 11787) +++ /issm/trunk-jpl/src/py/classes/geometry.py (revision 11787) @@ -0,0 +1,25 @@ +#module imports +from fielddisplay import fielddisplay + +class geometry: + #properties + def __init__(self): + # {{{ Properties + self.surface = float('NaN') + self.thickness = float('NaN') + self.bed = float('NaN') + self.bathymetry = float('NaN') + self.hydrostatic_ratio = float('NaN') + #}}} + def __repr__(obj): + # {{{ Display + + string=" geometry parameters:" + + string="%s\n\n%s"%(string,fielddisplay(obj,'surface','surface elevation')) + string="%s\n%s"%(string,fielddisplay(obj,'thickness','ice thickness')) + string="%s\n%s"%(string,fielddisplay(obj,'bed','bed elevation')) + string="%s\n%s"%(string,fielddisplay(obj,'bathymetry','bathymetry elevation')) + string="%s\n%s"%(string,fielddisplay(obj,'hydrostatic_ratio','coefficient for ice shelves'' thickness correction: hydrostatic_ratio H_obs+ (1-hydrostatic_ratio) H_hydro')) + return string + #}}} Index: /issm/trunk-jpl/src/py/classes/initialization.py =================================================================== --- /issm/trunk-jpl/src/py/classes/initialization.py (revision 11787) +++ /issm/trunk-jpl/src/py/classes/initialization.py (revision 11787) @@ -0,0 +1,32 @@ +#module imports +from fielddisplay import fielddisplay + +class initialization: + #properties + def __init__(self): + # {{{ Properties + + self.vx = float('NaN') + self.vy = float('NaN') + self.vz = float('NaN') + self.vel = float('NaN') + self.pressure = float('NaN') + self.temperature = float('NaN') + self.watercolumn = float('NaN') + self.waterfraction = float('NaN') + #}}} + def __repr__(obj): + # {{{ Display + string=' initial field values:' + + string="%s\n%s"%(string,fielddisplay(obj,'vx','x component of velocity')) + string="%s\n%s"%(string,fielddisplay(obj,'vy','y component of velocity')) + string="%s\n%s"%(string,fielddisplay(obj,'vz','z component of velocity')) + string="%s\n%s"%(string,fielddisplay(obj,'vel','velocity norm')) + string="%s\n%s"%(string,fielddisplay(obj,'pressure','pressure field')) + string="%s\n%s"%(string,fielddisplay(obj,'temperature','temperature in Kelvins')) + string="%s\n%s"%(string,fielddisplay(obj,'watercolumn','thickness of subglacial water')) + string="%s\n%s"%(string,fielddisplay(obj,'waterfraction','fraction of water in the ice')) + + return string + #}}} Index: /issm/trunk-jpl/src/py/classes/mask.py =================================================================== --- /issm/trunk-jpl/src/py/classes/mask.py (revision 11787) +++ /issm/trunk-jpl/src/py/classes/mask.py (revision 11787) @@ -0,0 +1,26 @@ +#module imports +from fielddisplay import fielddisplay + +class mask: + #properties + def __init__(self): + # {{{ Properties + self.elementonfloatingice = float('NaN') + self.elementongroundedice = float('NaN') + self.elementonwater = float('NaN') + self.vertexonfloatingice = float('NaN') + self.vertexongroundedice = float('NaN') + self.vertexonwater = float('NaN') + #}}} + def __repr__(obj): + # {{{ Display + + string=""; + string="%s\n%s"%(string,fielddisplay(obj,"elementonfloatingice","element on floating ice flags list")) + string="%s\n%s"%(string,fielddisplay(obj,"vertexonfloatingice","vertex on floating ice flags list")) + string="%s\n%s"%(string,fielddisplay(obj,"elementongroundedice","element on grounded ice list")) + string="%s\n%s"%(string,fielddisplay(obj,"vertexongroundedice","vertex on grounded ice flags list")) + string="%s\n%s"%(string,fielddisplay(obj,"elementonwater","element on water flags list")) + string="%s\n%s"%(string,fielddisplay(obj,"vertexonwater","vertex on water flags list")) + return string + #}}} Index: /issm/trunk-jpl/src/py/classes/materials.py =================================================================== --- /issm/trunk-jpl/src/py/classes/materials.py (revision 11787) +++ /issm/trunk-jpl/src/py/classes/materials.py (revision 11787) @@ -0,0 +1,41 @@ +#module imports +from fielddisplay import fielddisplay + +class materials: + #properties + def __init__(self): + # {{{ Properties + self.rho_ice = 0; + self.rho_water = 0; + self.mu_water = 0; + self.heatcapacity = 0; + self.latentheat = 0; + self.thermalconductivity = 0; + self.meltingpoint = 0; + self.beta = 0; + self.mixed_layer_capacity = 0; + self.thermal_exchange_velocity = 0; + self.rheology_B = float('NaN') + self.rheology_n = float('NaN') + self.rheology_law = ""; + #}}} + def __repr__(obj): + # {{{ Display + string=" Materials:" + + string="%s\n\n%s"%(string,fielddisplay(obj,"rho_ice","ice density [kg/m^3]")) + string="%s\n%s"%(string,fielddisplay(obj,"rho_water","water density [kg/m^3]")) + string="%s\n%s"%(string,fielddisplay(obj,"mu_water","water viscosity [N s/m^2]")) + string="%s\n%s"%(string,fielddisplay(obj,"heatcapacity","heat capacity [J/kg/K]")) + string="%s\n%s"%(string,fielddisplay(obj,"thermalconductivity","ice thermal conductivity [W/m/K]")) + string="%s\n%s"%(string,fielddisplay(obj,"meltingpoint","melting point of ice at 1atm in K")) + string="%s\n%s"%(string,fielddisplay(obj,"latentheat","latent heat of fusion [J/m^3]")) + string="%s\n%s"%(string,fielddisplay(obj,"beta","rate of change of melting point with pressure [K/Pa]")) + string="%s\n%s"%(string,fielddisplay(obj,"mixed_layer_capacity","mixed layer capacity [W/kg/K]")) + string="%s\n%s"%(string,fielddisplay(obj,"thermal_exchange_velocity","thermal exchange velocity [m/s]")) + string="%s\n%s"%(string,fielddisplay(obj,"rheology_B","flow law parameter [Pa/s^(1/n)]")) + string="%s\n%s"%(string,fielddisplay(obj,"rheology_n","Glen""s flow law exponent")) + string="%s\n%s"%(string,fielddisplay(obj,"rheology_law","law for the temperature dependance of the rheology: ""None"", ""Paterson"" or ""Arrhenius""")) + + return string + #}}} Index: /issm/trunk-jpl/src/py/classes/mesh.py =================================================================== --- /issm/trunk-jpl/src/py/classes/mesh.py (revision 11786) +++ /issm/trunk-jpl/src/py/classes/mesh.py (revision 11787) @@ -1,9 +1,108 @@ +#module imports +from fielddisplay import fielddisplay + class mesh: - """Python mesh class""" - x = [] - y = [] - elements = [] - def __repr__(self): - return """x: X coordinates - y: Y coordinates - elements: indexing """ + #properties + def __init__(self): + # {{{ Properties + self.x = float('NaN'); + self.y = float('NaN'); + self.z = float('NaN'); + self.elements = float('NaN'); + self.dimension = 0; + self.numberoflayers = 0; + self.numberofelements = 0; + self.numberofvertices = 0; + self.numberofedges = 0; + + self.lat = float('NaN'); + self.long = float('NaN'); + self.hemisphere = float('NaN'); + + self.elementonbed = float('NaN'); + self.elementonsurface = float('NaN'); + self.vertexonbed = float('NaN'); + self.vertexonsurface = float('NaN'); + self.lowerelements = float('NaN'); + self.lowervertex = float('NaN'); + self.upperelements = float('NaN'); + self.uppervertex = float('NaN'); + self.vertexonboundary = float('NaN'); + + self.edges = float('NaN'); + self.segments = float('NaN'); + self.segmentmarkers = float('NaN'); + self.vertexconnectivity = float('NaN'); + self.elementconnectivity = float('NaN'); + self.average_vertex_connectivity = 0; + + self.x2d = float('NaN'); + self.y2d = float('NaN'); + self.elements2d = float('NaN'); + self.numberofvertices2d = 0; + self.numberofelements2d = 0; + + self.extractedvertices = float('NaN'); + self.extractedelements = float('NaN'); + + #}}} + def __repr__(obj): + # {{{ Display + + if obj.dimension==3: + string="\n%s"%(" Elements and vertices of the original 2d mesh:") + + string="%s\n%s"%(string,fielddisplay(obj,"numberofelements2d","number of elements")) + string="%s\n%s"%(string,fielddisplay(obj,"numberofvertices2d","number of vertices")) + string="%s\n%s"%(string,fielddisplay(obj,"elements2d","index into (x,y,z), coordinates of the vertices")) + string="%s\n%s"%(string,fielddisplay(obj,"x2d","vertices x coordinate")) + string="%s\n%s"%(string,fielddisplay(obj,"y2d","vertices y coordinate")) + + string="%s\n%s" %(string,"Elements and vertices of the extruded 3d mesh:") + else: + string="\n%s"%(" Elements and vertices:") + + string="%s\n%s"%(string,fielddisplay(obj,"numberofelements","number of elements")) + + + + + string="%s\n%s"%(string,fielddisplay(obj,"numberofvertices","number of vertices")) + string="%s\n%s"%(string,fielddisplay(obj,"elements","index into (x,y,z), coordinates of the vertices")) + string="%s\n%s"%(string,fielddisplay(obj,"x","vertices x coordinate")) + string="%s\n%s"%(string,fielddisplay(obj,"y","vertices y coordinate")) + string="%s\n%s"%(string,fielddisplay(obj,"z","vertices z coordinate")) + string="%s\n%s"%(string,fielddisplay(obj,"edges","edges of the 2d mesh (vertex1 vertex2 element1 element2)")) + string="%s\n%s"%(string,fielddisplay(obj,"numberofedges","number of edges of the 2d mesh")) + + string="%s%s"%(string,"\n Properties:") + + string="%s\n%s"%(string,fielddisplay(obj,"dimension","mesh dimension (2d or 3d)")) + string="%s\n%s"%(string,fielddisplay(obj,"numberoflayers","number of extrusion layers")) + string="%s\n%s"%(string,fielddisplay(obj,"vertexonbed","lower vertices flags list")) + string="%s\n%s"%(string,fielddisplay(obj,"elementonbed","lower elements flags list")) + string="%s\n%s"%(string,fielddisplay(obj,"vertexonsurface","upper vertices flags list")) + string="%s\n%s"%(string,fielddisplay(obj,"elementonsurface","upper elements flags list")) + string="%s\n%s"%(string,fielddisplay(obj,"uppervertex","upper vertex list (NaN for vertex on the upper surface)")) + string="%s\n%s"%(string,fielddisplay(obj,"upperelements","upper element list (NaN for element on the upper layer)")) + string="%s\n%s"%(string,fielddisplay(obj,"lowervertex","lower vertex list (NaN for vertex on the lower surface)")) + string="%s\n%s"%(string,fielddisplay(obj,"lowerelements","lower element list (NaN for element on the lower layer")) + string="%s\n%s"%(string,fielddisplay(obj,"vertexonboundary","vertices on the boundary of the domain flag list")) + + string="%s\n%s"%(string,fielddisplay(obj,"segments","edges on domain boundary (vertex1 vertex2 element)")) + string="%s\n%s"%(string,fielddisplay(obj,"segmentmarkers","number associated to each segment")) + string="%s\n%s"%(string,fielddisplay(obj,"vertexconnectivity","list of vertices connected to vertex_i")) + string="%s\n%s"%(string,fielddisplay(obj,"elementconnectivity","list of vertices connected to element_i")) + string="%s\n%s"%(string,fielddisplay(obj,"average_vertex_connectivity","average number of vertices connected to one vertex")) + + string="%s%s"%(string,"\n Extracted model:") + + string="%s\n%s"%(string,fielddisplay(obj,"extractedvertices","vertices extracted from the model")) + string="%s\n%s"%(string,fielddisplay(obj,"extractedelements","elements extracted from the model")) + + string="%s%s"%(string,"\n Projection:") + string="%s\n%s"%(string,fielddisplay(obj,"lat","vertices latitude")) + string="%s\n%s"%(string,fielddisplay(obj,"long","vertices longitude")) + string="%s\n%s"%(string,fielddisplay(obj,"hemisphere","Indicate hemisphere ""n"" or ""s"" ")) + return string + #}}} Index: /issm/trunk-jpl/src/py/classes/model.py =================================================================== --- /issm/trunk-jpl/src/py/classes/model.py (revision 11786) +++ /issm/trunk-jpl/src/py/classes/model.py (revision 11787) @@ -1,9 +1,98 @@ -from mesh import * +#module imports {{{ +from mesh import mesh +from mask import mask +from geometry import geometry +from constants import constants +from surfaceforcings import surfaceforcings +from basalforcings import basalforcings +from materials import materials +from friction import friction +from flowequation import flowequation +from timestepping import timestepping +from initialization import initialization +from rifts import rifts +from debug import debug +from verbose import verbose +from settings import settings +from solver import solver +#}}} +class model: + #properties + def __init__(self): + # {{{ Properties + self.mesh = mesh() + self.mask = mask() + self.geometry = geometry() + self.constants = constants() + self.surfaceforcings = surfaceforcings() + self.basalforcings = basalforcings() + self.materials = materials() + self.friction = friction() + self.flowequation = flowequation() + self.timestepping = timestepping() + self.initialization = initialization() + self.rifts = rifts() -class model: - """Python model class""" - mesh=mesh() - def __init__(self): - print 'new model created' - def __repr__(self): - return " mesh: mesh properties" + self.debug = debug() + self.verbose = verbose() + self.settings = settings() + self.solver = solver() + self.cluster = []; + + self.balancethickness = []; + self.diagnostic = []; + self.groundingline = []; + self.hydrology = []; + self.prognostic = []; + self.thermal = []; + self.steadystate = []; + self.transient = []; + + self.autodiff = []; + self.flaim = []; + self.inversion = []; + self.qmu = []; + + self.results = []; + self.radaroverlay = []; + self.miscellaneous = []; + self.private = []; + #}}} + def __repr__(obj): + # {{{ Display + + #print "Here %s the number: %d" % ("is", 37) + string="%19s: %-22s -- %s" % ("mesh","[%s,%s]" % ("1x1",obj.mesh.__class__.__name__),"mesh properties") + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("mask","[%s,%s]" % ("1x1",obj.mask.__class__.__name__),"defines grounded and floating elements")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("geometry","[%s,%s]" % ("1x1",obj.geometry.__class__.__name__),"surface elevation, bedrock topography, ice thickness,...")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("constants","[%s,%s]" % ("1x1",obj.constants.__class__.__name__),"physical constants")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("surfaceforcings","[%s,%s]" % ("1x1",obj.surfaceforcings.__class__.__name__),"surface forcings")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("basalforcings","[%s,%s]" % ("1x1",obj.basalforcings.__class__.__name__),"bed forcings")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("materials","[%s,%s]" % ("1x1",obj.materials.__class__.__name__),"material properties")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("friction","[%s,%s]" % ("1x1",obj.friction.__class__.__name__),"basal friction/drag properties")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("flowequation","[%s,%s]" % ("1x1",obj.flowequation.__class__.__name__),"flow equations")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("timestepping","[%s,%s]" % ("1x1",obj.timestepping.__class__.__name__),"time stepping for transient models")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("initialization","[%s,%s]" % ("1x1",obj.initialization.__class__.__name__),"initial guess/state")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("rifts","[%s,%s]" % ("1x1",obj.rifts.__class__.__name__),"rifts properties'")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("debug","[%s,%s]" % ("1x1",obj.debug.__class__.__name__),"debugging tools (valgrind, gprof")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("verbose","[%s,%s]" % ("1x1",obj.verbose.__class__.__name__),"verbosity level in solve")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("settings","[%s,%s]" % ("1x1",obj.settings.__class__.__name__),"settings properties")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("solver","[%s,%s]" % ("1x1",obj.solver.__class__.__name__),"PETSc options for each solution'")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("cluster","[%s,%s]" % ("1x1",obj.cluster.__class__.__name__),"cluster parameters (number of cpus...)")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("balancethickness","[%s,%s]" % ("1x1",obj.balancethickness.__class__.__name__),"parameters for balancethickness solution")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("diagnostic","[%s,%s]" % ("1x1",obj.diagnostic.__class__.__name__),"parameters for diagnostic solution")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("groundingline","[%s,%s]" % ("1x1",obj.groundingline.__class__.__name__),"parameters for groundingline solution")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("hydrology","[%s,%s]" % ("1x1",obj.hydrology.__class__.__name__),"parameters for hydrology solution")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("prognostic","[%s,%s]" % ("1x1",obj.prognostic.__class__.__name__),"parameters for prognostic solution")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("thermal","[%s,%s]" % ("1x1",obj.thermal.__class__.__name__),"parameters for thermal solution")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("steadystate","[%s,%s]" % ("1x1",obj.steadystate.__class__.__name__),"parameters for steadystate solution")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("transient","[%s,%s]" % ("1x1",obj.transient.__class__.__name__),"parameters for transient solution")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("autodiff","[%s,%s]" % ("1x1",obj.autodiff.__class__.__name__),"automatic differentiation parameters")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("flaim","[%s,%s]" % ("1x1",obj.flaim.__class__.__name__),"flaim parameters")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("inversion","[%s,%s]" % ("1x1",obj.inversion.__class__.__name__),"parameters for inverse methods")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("qmu","[%s,%s]" % ("1x1",obj.qmu.__class__.__name__),"dakota properties")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("results","[%s,%s]" % ("1x1",obj.results.__class__.__name__),"model results'")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("radaroverlay","[%s,%s]" % ("1x1",obj.radaroverlay.__class__.__name__),"radar image for plot overlay")) + string="%s\n%s" % (string,"%19s: %-22s -- %s" % ("miscellaneous","[%s,%s]" % ("1x1",obj.miscellaneous.__class__.__name__),"miscellaneous fields")) + return string; + #}}} Index: /issm/trunk-jpl/src/py/classes/rifts.py =================================================================== --- /issm/trunk-jpl/src/py/classes/rifts.py (revision 11787) +++ /issm/trunk-jpl/src/py/classes/rifts.py (revision 11787) @@ -0,0 +1,18 @@ +#module imports +from fielddisplay import fielddisplay + +class rifts: + #properties + def __init__(self): + # {{{ Properties + self.riftstruct = float('NaN') + self.riftproperties = float('NaN') + #}}} + def __repr__(obj): + # {{{ Display + string=' rifts parameters:' + + string="%s\n\n%s"%(string,fielddisplay(obj,'riftstruct','structure containing all rift information (vertices coordinates, segments, type of melange, ...)')) + string="%s\n%s"%(string,fielddisplay(obj,'riftproperties','')) + return string + #}}} Index: /issm/trunk-jpl/src/py/classes/settings.py =================================================================== --- /issm/trunk-jpl/src/py/classes/settings.py (revision 11787) +++ /issm/trunk-jpl/src/py/classes/settings.py (revision 11787) @@ -0,0 +1,24 @@ +#module imports +from fielddisplay import fielddisplay + +class settings: + #properties + def __init__(self): + # {{{ Properties + self.io_gather = 0; + self.lowmem = 0; + self.results_as_patches = 0; + self.output_frequency = 0; + self.waitonlock = 0; + #}}} + def __repr__(obj): + # {{{ Display + string=" general settings parameters:" + + string="%s\n%s"%(string,fielddisplay(obj,"io_gather","I/O gathering strategy for result outputs (default 1)")) + string="%s\n%s"%(string,fielddisplay(obj,"lowmem","is the memory limited ? (0 or 1)")) + string="%s\n%s"%(string,fielddisplay(obj,"results_as_patches","provide results as patches for each element (0 or 1)")) + string="%s\n%s"%(string,fielddisplay(obj,"output_frequency","frequency at which results are saved in all solutions with multiple time_steps")) + string="%s\n%s"%(string,fielddisplay(obj,"waitonlock","maximum number of minutes to wait for batch results, or return 0")) + return string + #}}} Index: /issm/trunk-jpl/src/py/classes/solver.py =================================================================== --- /issm/trunk-jpl/src/py/classes/solver.py (revision 11787) +++ /issm/trunk-jpl/src/py/classes/solver.py (revision 11787) @@ -0,0 +1,42 @@ +#module imports +from fielddisplay import fielddisplay + +class solver: + #properties + def __init__(self): + # {{{ Properties + self.options = []; + #}}} + def __repr__(obj): + # {{{ Display + + string2=" solver parameters:" + for i in range(len(obj.options,1)): + option=obj.options[i] + analysis=option[0] + ioptions=option[1] + + string="" + for i in range(len(ioptions)): + option=ioptions[i] + if not option: + #do nothing + pass + elif len(option)==1: + #this option has only one argument + string="%s%s%s"%(string," -",option[0]) + elif len(option)==2: + #option with value. value can be string or scalar + if isinstance(option[1],float): + string="%s%s%s%s%s"%(string," -",option[0]," ","%g"%(option[1])) + elif isinstance(option[1],str): + string="%s%s%s%s%s"%(string," -",option[0]," ",option[1]) + else: + print("%s%s%s"%("PetscString error: option #","%i"%(i)," is not well formatted")) + sys.exit(); + else: + print("%s%s%s"%("PetscString error: option #","%i"%(i)," is not well formatted")) + sys.exit() + string2="%s\n%s"%(string2," %s -> '%s'"%(analysis,string)) + return string2 + #}}} Index: /issm/trunk-jpl/src/py/classes/surfaceforcings.py =================================================================== --- /issm/trunk-jpl/src/py/classes/surfaceforcings.py (revision 11787) +++ /issm/trunk-jpl/src/py/classes/surfaceforcings.py (revision 11787) @@ -0,0 +1,19 @@ +#module imports +from fielddisplay import fielddisplay + +class surfaceforcings: + #properties + def __init__(self): + # {{{ Properties + self.precipitation = float('NaN') + self.mass_balance = float('NaN') + #}}} + def __repr__(obj): + # {{{ Display + string=" surface forcings parameters:" + + string="%s\n\n%s"%(string,fielddisplay(obj,'precipitation','surface precipitation [m/yr water eq]')) + string="%s\n%s"%(string,fielddisplay(obj,'mass_balance','surface mass balance [m/yr ice eq]')) + + return string + #}}} Index: /issm/trunk-jpl/src/py/classes/timestepping.py =================================================================== --- /issm/trunk-jpl/src/py/classes/timestepping.py (revision 11787) +++ /issm/trunk-jpl/src/py/classes/timestepping.py (revision 11787) @@ -0,0 +1,21 @@ +#module imports +from fielddisplay import fielddisplay + +class timestepping: + #properties + def __init__(self): + # {{{ Properties + self.time_step = 0; + self.final_time = 0; + self.time_adapt = 0; + self.cfl_coefficient = 0; + #}}} + def __repr__(obj): + # {{{ Display + string=" timestepping parameters:" + string="%s\n\n%s"%(string,fielddisplay(obj,"time_step","length of time steps [yrs]")) + string="%s\n%s"%(string,fielddisplay(obj,"final_time","final time to stop the simulation [yrs]")) + string="%s\n%s"%(string,fielddisplay(obj,"time_adapt","use cfl condition to define time step ? (0 or 1) ")) + string="%s\n%s"%(string,fielddisplay(obj,"cfl_coefficient","coefficient applied to cfl condition")) + return string + #}}} Index: /issm/trunk-jpl/src/py/classes/verbose.py =================================================================== --- /issm/trunk-jpl/src/py/classes/verbose.py (revision 11787) +++ /issm/trunk-jpl/src/py/classes/verbose.py (revision 11787) @@ -0,0 +1,27 @@ +#module imports +from fielddisplay import fielddisplay + +class verbose: + #properties + def __init__(self): + # {{{ Properties + self.mprocessor = False + self.module = False + self.solution = False + self.solver = False + self.convergence = False + self.control = False + self.qmu = False + #}}} + def __repr__(obj): + # {{{ Display + string="%s%s%s\n\n"%("class '",obj.__class__.__name__,"'=") + string="%s%s\n"%(string," %15s : %s"%("mprocessor",obj.mprocessor)) + string="%s%s\n"%(string," %15s : %s"%("module",obj.module)) + string="%s%s\n"%(string," %15s : %s"%("solution",obj.solution)) + string="%s%s\n"%(string," %15s : %s"%("solver",obj.solver)) + string="%s%s\n"%(string," %15s : %s"%("convergence",obj.convergence)) + string="%s%s\n"%(string," %15s : %s"%("control",obj.control)) + string="%s%s\n"%(string," %15s : %s"%("qmu",obj.qmu)) + return string + #}}} Index: /issm/trunk-jpl/src/py/model/display/fielddisplay.py =================================================================== --- /issm/trunk-jpl/src/py/model/display/fielddisplay.py (revision 11787) +++ /issm/trunk-jpl/src/py/model/display/fielddisplay.py (revision 11787) @@ -0,0 +1,98 @@ +#Module import +from math import isnan + + +def fielddisplay(md,name,comment): +#FIELDDISPLAY - display model field +# +# Usage: +# fielddisplay(md,name,comment) + + #get field + field=getattr(md,name) + + #disp corresponding line as a function of field type (offset set as 9 spaces) + return parsedisplay(" ",name,field,comment); + +#parsedisplay{{{ +def parsedisplay(offset,name,field,comment): + + #string + if isinstance(field,str): + + if len(field)>30: + string=displayunit(offset,name,"not displayed",comment) + else: + string=displayunit(offset,name,field,comment) + + #numeric + elif isinstance(field, int): + string=displayunit(offset,name,"%i" % (field),comment) + + elif isinstance(field, complex): + print("fielddisplay cannot handle complex numbers") + sys.exit() + + elif isinstance(field, float): + string=displayunit(offset,name,"%g"%(field),comment) + + #logical + elif isinstance(field,bool): + if field: + string=displayunit(offset,name,"true",comment) + else: + string=displayunit(offset,name,"false",comment) + + #elif isstruct(field), + # if ~isempty(fields(field)) + # displayunit(offset,name,'(structure)',comment), + # struct_display(field,[offset ' ']), + # else + # displayunit(offset,name,'N/A',comment), + # end + + #cell + #elif iscell(field): + # cell_display(offset,name,field,comment), + + else: + string=displayunit(offset,name,"not displayed",comment) + + #return string + return string + +#}}} +#displayunit {{{ +def displayunit(offset,name,characterization,comment): + + #take care of name + if len(name)>23: + name="%s..." % (name[:19]) + + #take care of characterization + if characterization=="": + characterization="N/A" + + if characterization=="nan": + characterization="N/A" + + if len(characterization)>15: + characterization="%s%s" % (characterization[:11],"...") + + #print + if not comment: + string="%s%-23s: %-15s" % (offset,name,characterization) + else: + if isinstance(comment,str): + string="%s%-23s: %-15s -- %s" % (offset,name,characterization,comment) + elif isinstance(comment,list): + string="%s%-23s: %-15s -- %s" % (offset,name,characterization,comment[0]) + for i in range(2,len(comment)): + string2="%s%-23s %-15s %s" %(offset,"","",comment[i]) + string="%s%s"%(string,string2) + else: + print("fielddisplay error message: format for comment not supportet yet") + sys.exit() + + return string +#}}} Index: /issm/trunk-jpl/src/py/model/display/fielddisplay.rest =================================================================== --- /issm/trunk-jpl/src/py/model/display/fielddisplay.rest (revision 11787) +++ /issm/trunk-jpl/src/py/model/display/fielddisplay.rest (revision 11787) @@ -0,0 +1,154 @@ +def fielddisplay(md,name,comment): +#FIELDDISPLAY - display model field +# +# Usage: +# fielddisplay(md,offset,name,comment) + + #get field + field=getattr(md,name) + + #disp corresponding line as a function of field type (offset set as 9 spaces) + #parsedisplay(' ',name,field,comment); + + return + +function parsedisplay(offset,name,field,comment); %{{{ + + %string + if ischar(field), + + if length(field)>30; + displayunit(offset,name,'not displayed',comment), + else + displayunit(offset,name,['''' field ''''],comment), + end + + %numeric + elseif isnumeric(field) + + %get size + fieldsize=size(field); + + %double + if max(fieldsize)==1, + displayunit(offset,name,num2str(field),comment), + %matrix + else + displayunit(offset,name,['(' num2str(fieldsize(1)) 'x' num2str(fieldsize(2)) ')'],comment), + end + + %logical + elseif islogical(field) + + %get size + fieldsize=size(field); + + %single value + if max(fieldsize)==1, + if (field) + displayunit(offset,name,'true',comment), + else + displayunit(offset,name,'false',comment), + end + %matrix + else + displayunit(offset,name,['(' num2str(fieldsize(1)) 'x' num2str(fieldsize(2)) ')'],comment), + end + + %structure + elseif isstruct(field), + if ~isempty(fields(field)) + displayunit(offset,name,'(structure)',comment), + struct_display(field,[offset ' ']), + else + displayunit(offset,name,'N/A',comment), + end + + %cell + elseif iscell(field), + cell_display(offset,name,field,comment), + + else + displayunit(offset,name,'not displayed',comment), + + end +end%}}} + +function struct_display(structure,offset) % {{{ + + structure_fields=fields(structure); + + for i=1:length(structure_fields), + + %get current field + field=structure.(structure_fields{i}); + + %recursive call if necessary + if isstruct(field), + displayunit(offset,structure_fields{i},'(structure)',''), + struct_display(field,[offset ' ']); + + %display value + else + parsedisplay(offset,structure_fields{i},field,''); + end + end +end% }}} +function cell_display(offset,name,field,comment) % {{{ + + %initialization + string='{'; + + %go through the cell and fill string + if length(field)<5; + for i=1:length(field), + if ischar(field{i}), + string=[string '''' field{i} ''',']; + elseif (isnumeric(field{i}) & length(field{i})==1) + string=[string num2str(field{i}) ',' ]; + else + string='{'; + break + end + end + end + if strcmp(string,'{'), + string=['(' num2str(size(field,1)) 'x' num2str(size(field,2)) ')']; + else + string=[string(1:end-1) '}']; + end + + %call displayunit + displayunit(offset,name,string,comment); +end% }}} +function displayunit(offset,name,characterization,comment),% {{{ + + %take care of name + if length(name)>23, + name=[name(1:20) '...']; + end + + %take care of characterization + if (strcmp(characterization,['''' '''']) | strcmp(characterization,'NaN')), + characterization='N/A'; + end + if length(characterization)>15, + characterization=[characterization(1:12) '...']; + end + + %print + if isempty(comment) + disp(sprintf('%s%-23s: %-15s',offset,name,characterization)); + else + if ischar(comment), + disp(sprintf('%s%-23s: %-15s -- %s',offset,name,characterization,comment)); + elseif iscell(comment), + disp(sprintf('%s%-23s: %-15s -- %s',offset,name,characterization,comment{1})); + for i=2:length(comment), + disp(sprintf('%s%-23s %-15s %s',offset,'','',comment{i})); + end + else + error('fielddisplay error message: format for comment not supportet yet'); + end + end +end% }}} Index: /issm/trunk-jpl/src/py/modules/TriMesh/Makefile =================================================================== --- /issm/trunk-jpl/src/py/modules/TriMesh/Makefile (revision 11786) +++ /issm/trunk-jpl/src/py/modules/TriMesh/Makefile (revision 11787) @@ -1,18 +1,11 @@ -all: ogive +all: ice ice: g++ -bundle -bind \ -I$(ISSM_TIER)/externalpackages/boost/install/include \ + -I/Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m\ -L$(ISSM_TIER)/externalpackages/boost/install/lib -lboost_python \ - -L/usr/lib/python2.6/config/ -lpython2.6 \ + -L/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/config-3.2m/ -lpython3.2 \ TriMeshmodule.cpp -o TriMesh.so - -ogive: - g++ \ - -I$(ISSM_TIER)/externalpackages/boost/install/include \ - -I/opt/local/include/python2.5/ \ - -L$(ISSM_TIER)/externalpackages/boost/install/lib -lboost_python \ - -L/usr/lib/ -lpython2.5 \ - TriMeshmodule.cpp -o TriMesh.so -bundle clean: Index: /issm/trunk-jpl/src/py/modules/hello/Makefile =================================================================== --- /issm/trunk-jpl/src/py/modules/hello/Makefile (revision 11786) +++ /issm/trunk-jpl/src/py/modules/hello/Makefile (revision 11787) @@ -1,19 +1,13 @@ -all: ogive +all: ice ice: g++ -bundle -bind \ -I$(ISSM_TIER)/externalpackages/boost/install/include \ - -I/usr/include/python2.6/ \ + -I/Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m\ -L$(ISSM_TIER)/externalpackages/boost/install/lib -lboost_python \ - -L/usr/lib/python2.6/config/ -lpython2.6 \ + -L/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/config-3.2m/ -lpython3.2 \ hellomodule.cpp -o hello.so -ogive: - g++ \ - -I$(ISSM_TIER)/externalpackages/boost/install/include \ - -I/usr/include/python2.5/ \ - -L$(ISSM_TIER)/externalpackages/boost/install/lib -lboost_python \ - -L/usr/lib/python2.5/config/ -lpython2.5 \ - hellomodule.cpp -o hello.so -bundle + clean: Index: /issm/trunk-jpl/startup.py =================================================================== --- /issm/trunk-jpl/startup.py (revision 11786) +++ /issm/trunk-jpl/startup.py (revision 11787) @@ -10,4 +10,10 @@ import os,sys + +#First check we are running python 3 at least +if sys.version_info[0] < 3: + print("ISSM can only work in Python 3. Exiting python") + sys.exit(1) + #Recover ISSM_TIER, ISSM_DIR and USERNAME ISSM_TIER=os.getenv('ISSM_TIER') @@ -20,10 +26,38 @@ #the variable ISSM_TIER in this file, in case it is not correctly setup. -#ISSM path -sys.path.append(ISSM_TIER+'/src/py') -sys.path.append(ISSM_TIER+'/src/py/classes') -sys.path.append(ISSM_TIER+'/src/py/modules/TriMesh') -sys.path.append(ISSM_TIER+'/src/py/modules/hello') +#ISSM path. Go through src/py and load everything we find that looks like a python file +for root,dirs,files in os.walk(ISSM_TIER+ '/src/py'): + for file in files: + if file.find(".py") != -1: + if file.find(".pyc") == -1: + #add to path + sys.path.append(root) + file=os.path.splitext(file)[0] + #__import__(file) + +#Deal with scipy import: +import scipy +import numpy +import nose + +#Import modules that are absolutely needed in ISSM {{{ from model import * +from mesh import * +from mask import * +from geometry import * +from constants import * +from surfaceforcings import * +from basalforcings import * +from materials import * +from friction import * +from flowequation import * +from fielddisplay import * +from timestepping import * +from initialization import * +from rifts import * +from debug import * +from settings import * +from solver import * +#}}} -print "\n To get started with ISSM, type issmdoc at the command prompt.\n\n" +print("\n To get started with ISSM, type issmdoc at the command prompt.\n\n")