Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/solve.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/solve.py (revision 12943) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/solve.py (revision 12944) @@ -10,27 +10,27 @@ """ SOLVE - apply solution sequence for this model - Usage: - md=solve(md,solutionenum,varargin) - where varargin is a list of paired arguments of string OR enums + Usage: + md=solve(md,solutionenum,varargin) + where varargin is a list of paired arguments of string OR enums - solution types available comprise: - - DiagnosticSolutionEnum - - PrognosticSolutionEnum - - ThermalSolutionEnum - - SteadystateSolutionEnum - - TransientSolutionEnum... - - BalancethicknessSolutionEnum - - BedSlopeSolutionEnum - - SurfaceSlopeSolutionEnum - - HydrologySolutionEnum - - FlaimSolutionEnum + solution types available comprise: + - DiagnosticSolutionEnum + - PrognosticSolutionEnum + - ThermalSolutionEnum + - SteadystateSolutionEnum + - TransientSolutionEnum... + - BalancethicknessSolutionEnum + - BedSlopeSolutionEnum + - SurfaceSlopeSolutionEnum + - HydrologySolutionEnum + - FlaimSolutionEnum extra options: - - loadonly : does not solve. only load results + - loadonly : does not solve. only load results - Examples: - md=solve(md,DiagnosticSolutionEnum); + Examples: + md=solve(md,DiagnosticSolutionEnum); """ #recover and process solve options Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/process_solve_options.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/process_solve_options.py (revision 12943) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/process_solve_options.py (revision 12944) @@ -5,10 +5,10 @@ """ DEFAULT_SOLVE_OPTIONS - set up default options for solve phase - Usage: - options=process_solve_options(options) + Usage: + options=process_solve_options(options) - See also: SOLVE + See also: SOLVE """ outoptions={} Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/marshall.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/marshall.py (revision 12943) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/marshall.py (revision 12944) @@ -4,11 +4,11 @@ """ MARSHALL - outputs a compatible binary file from @model md, for certain solution type. - The routine creates a compatible binary file from @model md - This binary file will be used for parallel runs in JPL-package + The routine creates a compatible binary file from @model md + This binary file will be used for parallel runs in JPL-package - Usage: - marshall(md) + Usage: + marshall(md) """ print "marshalling file '%s.bin'." % md.miscellaneous.name Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/AnalysisConfiguration.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/AnalysisConfiguration.py (revision 12943) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/AnalysisConfiguration.py (revision 12944) @@ -4,8 +4,8 @@ """ ANALYSISCONFIGURATION - return type of analyses, number of analyses - Usage: - [analyses, numanalyses]=AnalysisConfiguration(solutiontype); + Usage: + [analyses, numanalyses]=AnalysisConfiguration(solutiontype); """ if solutiontype == DiagnosticSolutionEnum: Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/MatlabProcessPatch.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/MatlabProcessPatch.py (revision 12943) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/MatlabProcessPatch.py (revision 12944) @@ -2,8 +2,8 @@ """ PROCESSPATCH - create a structure from a patch - Usage: - Result=ProcessPatch(Result); + Usage: + Result=ProcessPatch(Result); """ #loop over steps Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/setflowequation.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/setflowequation.py (revision 12943) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/setflowequation.py (revision 12944) @@ -8,22 +8,22 @@ """ SETELEMENTSTYPE - associate a solution type to each element - This routine works like plotmodel: it works with an even number of inputs - 'hutter','macayeal','pattyn','stokes' and 'fill' are the possible options - that must be followed by the corresponding exp file or flags list - It can either be a domain file (argus type, .exp extension), or an array of element flags. - If user wants every element outside the domain to be - setflowequationd, add '~' to the name of the domain file (ex: '~Pattyn.exp'); - an empty string '' will be considered as an empty domain - a string 'all' will be considered as the entire domain - You can specify the type of coupling, 'penalties' or 'tiling', to use with the input 'coupling' + This routine works like plotmodel: it works with an even number of inputs + 'hutter','macayeal','pattyn','stokes' and 'fill' are the possible options + that must be followed by the corresponding exp file or flags list + It can either be a domain file (argus type, .exp extension), or an array of element flags. + If user wants every element outside the domain to be + setflowequationd, add '~' to the name of the domain file (ex: '~Pattyn.exp'); + an empty string '' will be considered as an empty domain + a string 'all' will be considered as the entire domain + You can specify the type of coupling, 'penalties' or 'tiling', to use with the input 'coupling' - Usage: - md=setflowequation(md,varargin) + Usage: + md=setflowequation(md,varargin) - Example: - md=setflowequation(md,'pattyn','Pattyn.exp','macayeal',md.mask.elementonfloatingice,'fill','hutter'); - md=setflowequation(md,'pattyn','Pattyn.exp',fill','hutter','coupling','tiling'); + Example: + md=setflowequation(md,'pattyn','Pattyn.exp','macayeal',md.mask.elementonfloatingice,'fill','hutter'); + md=setflowequation(md,'pattyn','Pattyn.exp',fill','hutter','coupling','tiling'); """ #some checks on list of arguments Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/loadresultsfromdisk.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/loadresultsfromdisk.py (revision 12943) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/loadresultsfromdisk.py (revision 12944) @@ -4,8 +4,8 @@ """ LOADRESULTSFROMDISK - load results of solution sequence from disk file "filename" - Usage: - md=loadresultsfromdisk(md=False,filename=False); + Usage: + md=loadresultsfromdisk(md=False,filename=False); """ #check number of inputs/outputs Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/waitonlock.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/waitonlock.py (revision 12943) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/waitonlock.py (revision 12944) @@ -7,11 +7,11 @@ """ WAITONLOCK - wait for a file - This routine will return when a file named 'filename' is written to disk. - If the time limit given in input is exceeded, return 0 + This routine will return when a file named 'filename' is written to disk. + If the time limit given in input is exceeded, return 0 - Usage: - flag=waitonlock(md,executionpath) + Usage: + flag=waitonlock(md,executionpath) """ #Get filename (lock file) and options Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/recover_areas.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/recover_areas.py (revision 12943) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/recover_areas.py (revision 12944) @@ -5,10 +5,10 @@ """ RECOVER_AREAS - flag the element depending on the physical model that is assigned to them - This routine is called by setelementstype, do not use + This routine is called by setelementstype, do not use - Usage: - [hutterflag macayealflag pattynflag stokesflag filltype]=recover_areas(md,varargin); + Usage: + [hutterflag macayealflag pattynflag stokesflag filltype]=recover_areas(md,varargin); """ #go through varargin, extract options and plug them into subtype options, by order of appearance Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/WriteData.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/WriteData.py (revision 12943) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/WriteData.py (revision 12944) @@ -7,8 +7,8 @@ """ WRITEDATA - write model field in binary file - Usage: - WriteData(fid,varargin) + Usage: + WriteData(fid,varargin) """ #process options Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/loadresultsfromcluster.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/loadresultsfromcluster.py (revision 12943) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/loadresultsfromcluster.py (revision 12944) @@ -7,8 +7,8 @@ """ LOADRESULTSFROMCLUSTER - load results of solution sequence from cluster - Usage: - md=loadresultsfromcluster(md,runtimename); + Usage: + md=loadresultsfromcluster(md,runtimename); """ #retrieve cluster, to be able to call its methods Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/parameterization/parameterize.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/parameterization/parameterize.py (revision 12943) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/parameterization/parameterize.py (revision 12944) @@ -5,16 +5,16 @@ def parameterize(md,parametername): """ PARAMETERIZE - parameterize a model - - from a parameter python file, start filling in all the model fields that were not - filled in by the mesh.py and mask.py model methods. - Warning: the parameter file must be able to be run in Python - - Usage: - md=parameterize(md,parametername) - - Example: - md=parameterize(md,'Square.par'); + + from a parameter python file, start filling in all the model fields that were not + filled in by the mesh.py and mask.py model methods. + Warning: the parameter file must be able to be run in Python + + Usage: + md=parameterize(md,parametername) + + Example: + md=parameterize(md,'Square.par'); """ #some checks Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/parseresultsfromdisk.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/parseresultsfromdisk.py (revision 12943) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/parseresultsfromdisk.py (revision 12944) @@ -6,9 +6,9 @@ def parseresultsfromdisk(filename,iosplit): """ PARSERESULTSFROMDISK - ... - - Usage: - results=parseresultsfromdisk(filename,iosplit) + + Usage: + results=parseresultsfromdisk(filename,iosplit) """ if iosplit: Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/addnote.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/addnote.py (revision 12943) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/addnote.py (revision 12944) @@ -1,12 +1,12 @@ def addnote(md,string): """ ADDNOTE - add a note to the existing model notes field - - Usage: - md=addnote(md,string); - - Example: - md=addnote(md,'Pine Island, Geometry of 2007'); + + Usage: + md=addnote(md,string); + + Example: + md=addnote(md,'Pine Island, Geometry of 2007'); """ if not isinstance(string,str): Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/ismodelselfconsistent.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/ismodelselfconsistent.py (revision 12943) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/ismodelselfconsistent.py (revision 12944) @@ -4,8 +4,8 @@ """ ISMODELSELFCONSISTENT - check that model forms a closed form solvable problem. - Usage: - ismodelselfconsistent(md), + Usage: + ismodelselfconsistent(md), """ #initialize consistency as true Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/petscversion.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/petscversion.py (revision 12943) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/model/petscversion.py (revision 12944) @@ -6,8 +6,8 @@ """ PETSCVERSION - recover petsc version number, inside config.h file - Usage: - PETSC_VERSION=petscversion(); + Usage: + PETSC_VERSION=petscversion(); """ #default Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/utils/OS/issmscpin.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/utils/OS/issmscpin.py (revision 12943) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/utils/OS/issmscpin.py (revision 12944) @@ -9,9 +9,7 @@ """ SCPIN get packages from host, using scp on unix, and pscp on windows - usage: scpin(host,packages,path) - - + usage: scpin(host,packages,path) """ #first get hostname Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/utils/OS/issmscpout.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/utils/OS/issmscpout.py (revision 12943) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/utils/OS/issmscpout.py (revision 12944) @@ -9,9 +9,7 @@ """ SCPOUT send packages to a host, using scp on unix, and pscp on windows - usage: scpout(host,path,packages) - - + usage: scpout(host,path,packages) """ #get hostname Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/utils/OS/issmssh.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/utils/OS/issmssh.py (revision 12943) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/utils/OS/issmssh.py (revision 12944) @@ -8,8 +8,8 @@ """ ISSMSSH - wrapper for OS independent ssh command. - usage: - issmssh(host,command) + usage: + issmssh(host,command) """ #first get hostname Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/utils/OS/ispetsc.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/utils/OS/ispetsc.py (revision 12943) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/utils/OS/ispetsc.py (revision 12944) @@ -6,8 +6,8 @@ """ ISPETSC - figure out if PETSC package was compiled with ISSM - Usage: - flag=ispetsc(); + Usage: + flag=ispetsc(); """ configfile=os.path.join(issmdir(),'bin','config.h') #should find it in the install target Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/utils/OS/ismumps.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/utils/OS/ismumps.py (revision 12943) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/utils/OS/ismumps.py (revision 12944) @@ -6,8 +6,8 @@ """ ISMUMPS - figure out if MUMPS package was compiled with ISSM - Usage: - flag=ismumps(); + Usage: + flag=ismumps(); """ configfile=os.path.join(issmdir(),'bin','config.h') #should find it in the install target Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/utils/Cluster/parallelrange.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/utils/Cluster/parallelrange.py (revision 12943) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/utils/Cluster/parallelrange.py (revision 12944) @@ -3,8 +3,8 @@ """ PARALLELRANGE - from a rank, and a number of processors, figure out a range, for parallel tasks. - Usage: - i1,i2=parallelrange(rank,numprocs,globalsize) + Usage: + i1,i2=parallelrange(rank,numprocs,globalsize) """ #We use floor. we under distribute rows. The rows left are then redistributed, therefore resulting in a more even distribution. Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/utils/BC/SetIceShelfBC.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/utils/BC/SetIceShelfBC.py (revision 12943) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/utils/BC/SetIceShelfBC.py (revision 12944) @@ -4,19 +4,19 @@ def SetIceShelfBC(md,icefrontfile=''): """ SETICESHELFBC - Create the boundary conditions for diagnostic and thermal models for a Ice Shelf with Ice Front - - Neumann BC are used on the ice front (an ANRGUS contour around the ice front - must be given in input) - Dirichlet BC are used elsewhere for diagnostic - - Usage: - md=SetIceShelfBC(md,varargin) - - Example: - md=SetIceShelfBC(md); - md=SetIceShelfBC(md,'Front.exp'); - - See also: SETICESHEETBC, SETMARINEICESHEETBC + + Neumann BC are used on the ice front (an ANRGUS contour around the ice front + must be given in input) + Dirichlet BC are used elsewhere for diagnostic + + Usage: + md=SetIceShelfBC(md,varargin) + + Example: + md=SetIceShelfBC(md); + md=SetIceShelfBC(md,'Front.exp'); + + See also: SETICESHEETBC, SETMARINEICESHEETBC """ #node on Dirichlet (boundary and ~icefront) Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/utils/Geometry/FlagElements.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/utils/Geometry/FlagElements.py (revision 12943) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/utils/Geometry/FlagElements.py (revision 12944) @@ -8,17 +8,17 @@ """ FLAGELEMENTS - flag the elements in an region - The region can be given with an exp file, a list of elements. + The region can be given with an exp file, a list of elements. - Usage: - flag=FlagElements(md,region); + Usage: + flag=FlagElements(md,region); - Example: - flag=FlagElements(md,'all'); - flag=FlagElements(md,''); - flag=FlagElements(md,'Domain.exp'); - flag=FlagElements(md,'~Domain.exp'); - flag=FlagElements(md,md.mask.elementongroundedice); + Example: + flag=FlagElements(md,'all'); + flag=FlagElements(md,''); + flag=FlagElements(md,'Domain.exp'); + flag=FlagElements(md,'~Domain.exp'); + flag=FlagElements(md,md.mask.elementongroundedice); """ if isinstance(region,str): Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/utils/Shell/issmdir.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/utils/Shell/issmdir.py (revision 12943) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/utils/Shell/issmdir.py (revision 12944) @@ -6,8 +6,8 @@ """ ISSMDIR - Get ISSM_DIR environment variable - Usage: - ISSM_DIR=issmdir() + Usage: + ISSM_DIR=issmdir() """ if not 'Windows' in platform.system(): Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/clusters/generic.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/clusters/generic.py (revision 12943) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/clusters/generic.py (revision 12944) @@ -13,9 +13,9 @@ """ GENERIC cluster class definition - Usage: - cluster=generic('name','astrid','np',3); - cluster=generic('name',oshostname(),'np',3,'login','username'); + Usage: + cluster=generic('name','astrid','np',3); + cluster=generic('name',oshostname(),'np',3,'login','username'); """ def __init__(self,*args): # {{{ Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/pairoptions.py =================================================================== --- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/pairoptions.py (revision 12943) +++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/m/classes/pairoptions.py (revision 12944) @@ -4,9 +4,9 @@ """ PAIROPTIONS class definition - Usage: - pairoptions=pairoptions(); - pairoptions=pairoptions('module',true,'solver',false); + Usage: + pairoptions=pairoptions(); + pairoptions=pairoptions('module',true,'solver',false); """ def __init__(self,*arg):