Index: /issm/trunk-jpl/src/m/classes/SMBgradientscomponents.m =================================================================== --- /issm/trunk-jpl/src/m/classes/SMBgradientscomponents.m (revision 23365) +++ /issm/trunk-jpl/src/m/classes/SMBgradientscomponents.m (revision 23365) @@ -0,0 +1,90 @@ +%SMBgradientscomponents Class definition +% +% Usage: +% SMBgradientscomponents=SMBgradientscomponents(); + +classdef SMBgradientscomponents + properties (SetAccess=public) + accuref = NaN; + accualti = NaN; + accugrad = NaN; + runoffref = NaN; + runoffalti = NaN; + runoffgrad = NaN; + requested_outputs = {}; + end + methods + function self=SMBgradientscomponents(varargin) % {{{ + switch nargin + case 0 + self=setdefaultparameters(self); + otherwise + error('constructor not supported'); + end + end % }}} + + function self = extrude(self,md) % {{{ + + %Nothing for now + + end % }}} + function list = defaultoutputs(self,md) % {{{ + list = {'runoff'}; + end % }}} + function self = initialize(self,md) % {{{ + + %Nothing done for now + + end % }}} + function self = setdefaultparameters(self) % {{{ + + %Nothing for now + + end % }}} + function md=checkconsistency(self,md,solution,analyses) % {{{ + if ismember('MasstransportAnalysis',analyses), + md = checkfield(md,'fieldname','smb.accuref','timeseries',1,'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','smb.accualti','numel',1,'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','smb.accugrad','numel',1,'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','smb.runoffref','timeseries',1,'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','smb.runoffalti','numel',1,'NaN',1,'Inf',1); + md = checkfield(md,'fieldname','smb.runoffgrad','numel',1,'NaN',1,'Inf',1); + end + md = checkfield(md,'fieldname','masstransport.requested_outputs','stringrow',1); + end % }}} + + function disp(self) % {{{ + disp(sprintf(' surface forcings parameters:')); + disp(sprintf('\n SMB gradients components parameters:')); + fielddisplay(self,'accuref',' reference value of the accumulation'); + fielddisplay(self,'accualti',' Altitude at which the accumulation is equal to the reference value'); + fielddisplay(self,'accugrad',' Gradient of the variation of the accumulation (0 for uniform accumulation)'); + fielddisplay(self,'runoffref',' reference value of the runoff m w.e. y-1 (temperature times ddf)'); + fielddisplay(self,'runoffalti',' Altitude at which the runoff is equal to the reference value'); + fielddisplay(self,'runoffgrad',' Gradient of the variation of the runoff (0 for uniform runoff) m w.e. m-1 y-1 (lpase rate times ddf)'); + fielddisplay(self,'requested_outputs','additional outputs requested'); + + end % }}} + function marshall(self,prefix,md,fid) % {{{ + + WriteData(fid,prefix,'name','md.smb.model','data',11,'format','Integer'); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','accuref','format','DoubleMat','mattype',1,'timeserieslength',2,'yts',md.constants.yts,'scale',1./md.constants.yts); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','accualti','format','Double'); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','accugrad','format','Double','scale',1./md.constants.yts); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','runoffref','format','DoubleMat','mattype',1,'timeserieslength',2,'yts',md.constants.yts,'scale',1./md.constants.yts); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','runoffalti','format','Double'); + WriteData(fid,prefix,'object',self,'class','smb','fieldname','runoffgrad', ... + 'format','Double','scale',1./md.constants.yts); + + %process requested outputs + outputs = self.requested_outputs; + pos = find(ismember(outputs,'default')); + if ~isempty(pos), + outputs(pos) = []; %remove 'default' from outputs + outputs = [outputs defaultoutputs(self,md)]; %add defaults + end + WriteData(fid,prefix,'data',outputs,'name','md.smb.requested_outputs','format','StringArray'); + + end % }}} + end +end Index: /issm/trunk-jpl/src/m/classes/SMBgradientscomponents.py =================================================================== --- /issm/trunk-jpl/src/m/classes/SMBgradientscomponents.py (revision 23365) +++ /issm/trunk-jpl/src/m/classes/SMBgradientscomponents.py (revision 23365) @@ -0,0 +1,78 @@ +from fielddisplay import fielddisplay +from checkfield import checkfield +from WriteData import WriteData +from project3d import project3d + +class SMBgradientscomponents(object): + """ + SMBgradients Class definition + + Usage: + SMBgradients=SMBgradientscomponents(); + For now it has accumulation, runoff ans retention which could be aither refreezing and/or evaporation + """ + + def __init__(self): # {{{ + self.accuref = float('NaN') + self.accualti = float('NaN') + self.accugrad = float('NaN') + self.runoffref = float('NaN') + self.runoffalti = float('NaN') + self.runoffgrad = float('NaN') + self.requested_outputs = ['default'] + #}}} + def __repr__(self): # {{{ + string=" surface forcings parameters:" + string="%s\n%s"%(string,fielddisplay(self,'accuref',' reference value of the accumulation')) + string="%s\n%s"%(string,fielddisplay(self,'accualti',' Altitude at which the accumulation is equal to the reference value')) + string="%s\n%s"%(string,fielddisplay(self,'accugrad',' Gradient of the variation of the accumulation (0 for uniform accumulation)')) + string="%s\n%s"%(string,fielddisplay(self,'runoffref',' reference value of the runoff m w.e. y-1 (temperature times ddf)')) + string="%s\n%s"%(string,fielddisplay(self,'runoffalti',' Altitude at which the runoff is equal to the reference value')) + string="%s\n%s"%(string,fielddisplay(self,'runoffgrad',' Gradient of the variation of the runoff (0 for uniform runoff) m w.e. m-1 y-1 (lpase rate times ddf)')) + string="%s\n%s"%(string,fielddisplay(self,'requested_outputs','additional outputs requested')) + + return string + #}}} + def extrude(self,md): # {{{ + #Nothing for now + return self + #}}} + def defaultoutputs(self,md): # {{{ + return ['SmbMassBalance','SmbRunoff'] + #}}} + def initialize(self,md): # {{{ + #Nothing for now + return self + #}}} + def checkconsistency(self,md,solution,analyses): # {{{ + if 'MasstransportAnalysis' in analyses: + md = checkfield(md,'fieldname','smb.accuref','singletimeseries',1,'NaN',1,'Inf',1) + md = checkfield(md,'fieldname','smb.accualti','numel',[1],'NaN',1,'Inf',1) + md = checkfield(md,'fieldname','smb.accugrad','numel',[1],'NaN',1,'Inf',1) + md = checkfield(md,'fieldname','smb.runoffref','singletimeseries',1,'NaN',1,'Inf',1) + md = checkfield(md,'fieldname','smb.runoffalti','numel',[1],'NaN',1,'Inf',1) + md = checkfield(md,'fieldname','smb.runoffgrad','numel',[1],'NaN',1,'Inf',1) + md = checkfield(md,'fieldname','masstransport.requested_outputs','stringrow',1) + return md + # }}} + def marshall(self,prefix,md,fid): # {{{ + + yts=md.constants.yts + + WriteData(fid,prefix,'name','md.smb.model','data',11,'format','Integer') + WriteData(fid,prefix,'object',self,'class','smb','fieldname','accuref','format','DoubleMat','mattype',1,'timeserieslength',2,'yts',md.constants.yts,'scale',1./md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','accualti','format','Double') + WriteData(fid,prefix,'object',self,'class','smb','fieldname','accugrad','format','Double','scale',1./md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','runoffref','format','DoubleMat','mattype',1,'timeserieslength',2,'yts',md.constants.yts,'scale',1./md.constants.yts) + WriteData(fid,prefix,'object',self,'class','smb','fieldname','runoffalti','format','Double') + WriteData(fid,prefix,'object',self,'class','smb','fieldname','runoffgrad','format','Double','scale',1./md.constants.yts) + + #process requested outputs + outputs = self.requested_outputs + indices = [i for i, x in enumerate(outputs) if x == 'default'] + if len(indices) > 0: + outputscopy=outputs[0:max(0,indices[0]-1)]+self.defaultoutputs(md)+outputs[indices[0]+1:] + outputs =outputscopy + WriteData(fid,prefix,'data',outputs,'name','md.smb.requested_outputs','format','StringArray') + + # }}} Index: /issm/trunk-jpl/src/m/classes/clusters/stallo.m =================================================================== --- /issm/trunk-jpl/src/m/classes/clusters/stallo.m (revision 23364) +++ /issm/trunk-jpl/src/m/classes/clusters/stallo.m (revision 23365) @@ -105,7 +105,9 @@ fprintf(fid,'#SBATCH --nodes=%i \n',cluster.numnodes); fprintf(fid,'#SBATCH --ntasks-per-node=%i \n',cluster.cpuspernode); - fprintf(fid,'#SBATCH --time=%02i-%02i:%02i:00 \n',floor(cluster.time/(3600*24)),floor(cluster.time/3600),floor(mod(cluster.time,60))); - fprintf(fid,'#SBATCH --mem-per-cpu=%iMB\n',1000*cluster.mem); ... - % mem in MB + days=floor(cluster.time/(60*24)); + hours=floor((cluster.time-(days*60*24))/60); + minutes=floor(mod((cluster.time-(days*60*24)-(hours*60)),60)); + fprintf(fid,'#SBATCH --time=%02i-%02i:%02i:00 \n',days,hours,minutes); + fprintf(fid,'#SBATCH --mem-per-cpu=%iMB\n',1000*cluster.mem); % mem in MB if (mod(cluster.np,16)+mod(cluster.np,20))==0, fprintf(fid,'#SBATCH --ntask=%i\n',cluster.np); Index: /issm/trunk-jpl/src/m/classes/clusters/stallo.py =================================================================== --- /issm/trunk-jpl/src/m/classes/clusters/stallo.py (revision 23364) +++ /issm/trunk-jpl/src/m/classes/clusters/stallo.py (revision 23365) @@ -120,7 +120,7 @@ h,m=divmod(m, 60) d,h=divmod(h, 60) -# timestring="%02d-%02d:%02d:%02d" % (d, h, m, s) + timestring="%02d-%02d:%02d:%02d" % (d, h, m, s) fid.write('#SBATCH --time={}\n'.format(timestring)) #walltime is minutes - fid.write('#SBATCH --mem-per-cpu={}MB\n'.format(1000*self.mem))# mem is in MB (to keep it integral) + fid.write('#SBATCH --mem-per-cpu={}MB\n'.format(int(1000*self.mem)))# mem is in MB (to keep it integral) if (np.mod(self.np,16)+np.mod(self.np,20))==0: fid.write('#SBATCH --ntask=%i\n' % self.np) Index: /issm/trunk-jpl/src/m/classes/taoinversion.py =================================================================== --- /issm/trunk-jpl/src/m/classes/taoinversion.py (revision 23364) +++ /issm/trunk-jpl/src/m/classes/taoinversion.py (revision 23365) @@ -97,5 +97,5 @@ else: self.algorithm = 'tao_blmvm'; - + #several responses can be used: self.cost_functions=101; @@ -110,8 +110,8 @@ if numel(self.cost_functions_coefficients) > 1: self.cost_functions_coefficients=project3d(md,'vector',self.cost_functions_coefficients,'type','node') - + if numel(self.min_parameters) > 1: self.min_parameters=project3d(md,'vector',self.min_parameters,'type','node') - + if numel(self.max_parameters)>1: self.max_parameters=project3d(md,'vector',self.max_parameters,'type','node') @@ -123,5 +123,5 @@ return md if not IssmConfig('_HAVE_TAO_')[0]: - md = checkmessage(md,['TAO has not been installed, ISSM needs to be reconfigured and recompiled with TAO']) + md = md.checkmessage('TAO has not been installed, ISSM needs to be reconfigured and recompiled with TAO') Index: /issm/trunk-jpl/src/m/contrib/defleurian/paraview/enveloppeVTK.py =================================================================== --- /issm/trunk-jpl/src/m/contrib/defleurian/paraview/enveloppeVTK.py (revision 23364) +++ /issm/trunk-jpl/src/m/contrib/defleurian/paraview/enveloppeVTK.py (revision 23365) @@ -85,5 +85,5 @@ if (np.size(res_struct.__dict__[solution])>num_of_timesteps): num_of_timesteps=np.size(res_struct.__dict__[solution]) - num_of_timesteps=int(num_of_timesteps)+1 + num_of_timesteps=int(num_of_timesteps) else: num_of_timesteps=1 @@ -125,5 +125,5 @@ #getting the fields in the solution if(np.size(res_struct.__dict__[sol])>1): - fieldnames=dict.keys(res_struct.__dict__[sol].__getitem__(timestep-1).__dict__) + fieldnames=dict.keys(res_struct.__dict__[sol].__getitem__(timestep).__dict__) else: fieldnames=dict.keys(res_struct.__dict__[sol].__dict__) @@ -131,5 +131,5 @@ for field in fieldnames: if(np.size(res_struct.__dict__[sol])>1): - fieldstruct=res_struct.__dict__[sol].__getitem__(timestep-1).__dict__[field] + fieldstruct=res_struct.__dict__[sol].__getitem__(timestep).__dict__[field] else: fieldstruct=res_struct.__dict__[sol].__dict__[field] Index: /issm/trunk-jpl/src/m/solve/WriteData.py =================================================================== --- /issm/trunk-jpl/src/m/solve/WriteData.py (revision 23364) +++ /issm/trunk-jpl/src/m/solve/WriteData.py (revision 23365) @@ -7,5 +7,5 @@ """ WRITEDATA - write model field in binary file - + Usage: WriteData(fid,varargin) @@ -57,5 +57,5 @@ #Step 1: write the enum to identify this record uniquely fid.write(struct.pack('i',len(name))) - fid.write(struct.pack('%ds' % len(name),name)) + fid.write(struct.pack('%ds' % len(name),name)) #Step 2: write the data itself. @@ -67,6 +67,6 @@ fid.write(struct.pack('i',4+4)) #1 bool (disguised as an int)+code - #write data code: - fid.write(struct.pack('i',FormatToCode(format))) + #write data code: + fid.write(struct.pack('i',FormatToCode(format))) #now write integer @@ -81,9 +81,9 @@ fid.write(struct.pack('i',4+4)) #1 integer + code - #write data code: - fid.write(struct.pack('i',FormatToCode(format))) + #write data code: + fid.write(struct.pack('i',FormatToCode(format))) #now write integer - fid.write(struct.pack('i',data)) + fid.write(struct.pack('i',data)) # }}} @@ -95,9 +95,9 @@ fid.write(struct.pack('i',8+4)) #1 double+code - #write data code: - fid.write(struct.pack('i',FormatToCode(format))) + #write data code: + fid.write(struct.pack('i',FormatToCode(format))) #now write double - fid.write(struct.pack('d',data)) + fid.write(struct.pack('d',data)) # }}} @@ -106,10 +106,10 @@ fid.write(struct.pack('i',len(data)+4+4)) #string + string size + code - #write data code: - fid.write(struct.pack('i',FormatToCode(format))) + #write data code: + fid.write(struct.pack('i',FormatToCode(format))) #now write string - fid.write(struct.pack('i',len(data))) - fid.write(struct.pack('%ds' % len(data),data)) + fid.write(struct.pack('i',len(data))) + fid.write(struct.pack('%ds' % len(data),data)) # }}} @@ -135,17 +135,17 @@ fid.write(struct.pack('i',4+4+8*np.product(s)+4+4)) #2 integers (32 bits) + the double matrix + code + matrix type - #write data code and matrix type: - fid.write(struct.pack('i',FormatToCode(format))) + #write data code and matrix type: + fid.write(struct.pack('i',FormatToCode(format))) fid.write(struct.pack('i',mattype)) #now write matrix if np.ndim(data)==1: - fid.write(struct.pack('i',s[0])) - fid.write(struct.pack('i',1)) + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',1)) for i in xrange(s[0]): fid.write(struct.pack('d',float(data[i]))) #get to the "c" convention, hence the transpose else: - fid.write(struct.pack('i',s[0])) - fid.write(struct.pack('i',s[1])) + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',s[1])) for i in xrange(s[0]): for j in xrange(s[1]): @@ -174,17 +174,17 @@ fid.write(struct.pack('i',4+4+8*np.product(s)+4+4)) #2 integers (32 bits) + the double matrix + code + matrix type - #write data code and matrix type: - fid.write(struct.pack('i',FormatToCode(format))) + #write data code and matrix type: + fid.write(struct.pack('i',FormatToCode(format))) fid.write(struct.pack('i',mattype)) #now write matrix if np.ndim(data) == 1: - fid.write(struct.pack('i',s[0])) - fid.write(struct.pack('i',1)) + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',1)) for i in xrange(s[0]): fid.write(struct.pack('d',float(data[i]))) #get to the "c" convention, hence the transpose else: - fid.write(struct.pack('i',s[0])) - fid.write(struct.pack('i',s[1])) + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',s[1])) for i in xrange(s[0]): for j in xrange(s[1]): @@ -217,17 +217,17 @@ fid.write(struct.pack('i',recordlength)) #2 integers (32 bits) + the double matrix + code + matrix type - #write data code and matrix type: - fid.write(struct.pack('i',FormatToCode(format))) + #write data code and matrix type: + fid.write(struct.pack('i',FormatToCode(format))) fid.write(struct.pack('i',mattype)) #now write matrix if np.ndim(data) == 1: - fid.write(struct.pack('i',s[0])) - fid.write(struct.pack('i',1)) + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',1)) for i in xrange(s[0]): fid.write(struct.pack('d',float(data[i]))) #get to the "c" convention, hence the transpose else: - fid.write(struct.pack('i',s[0])) - fid.write(struct.pack('i',s[1])) + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',s[1])) for i in xrange(s[0]): for j in xrange(s[1]): @@ -266,6 +266,6 @@ fid.write(struct.pack('i',recordlength)) #2 integers (32 bits) + the matrix + code + matrix type - #write data code and matrix type: - fid.write(struct.pack('i',FormatToCode(format))) + #write data code and matrix type: + fid.write(struct.pack('i',FormatToCode(format))) fid.write(struct.pack('i',mattype)) @@ -276,12 +276,12 @@ if rangeA == 0: - A = A*0 - else: - A = (A-offsetA)/rangeA*255. - + A = A*0 + else: + A = (A-offsetA)/rangeA*255. + #now write matrix if np.ndim(data) == 1: - fid.write(struct.pack('i',s[0])) - fid.write(struct.pack('i',1)) + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',1)) fid.write(struct.pack('d',float(offsetA))) fid.write(struct.pack('d',float(rangeA))) @@ -292,6 +292,6 @@ elif np.product(s) > 0: - fid.write(struct.pack('i',s[0])) - fid.write(struct.pack('i',s[1])) + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',s[1])) fid.write(struct.pack('d',float(offsetA))) fid.write(struct.pack('d',float(rangeA))) @@ -324,11 +324,11 @@ #write length of record - fid.write(struct.pack('i',recordlength)) - - #write data code: - fid.write(struct.pack('i',FormatToCode(format))) + fid.write(struct.pack('i',recordlength)) + + #write data code: + fid.write(struct.pack('i',FormatToCode(format))) #write data, first number of records - fid.write(struct.pack('i',len(data))) + fid.write(struct.pack('i',len(data))) for matrix in data: @@ -343,11 +343,11 @@ if np.ndim(matrix) == 1: - fid.write(struct.pack('i',s[0])) - fid.write(struct.pack('i',1)) + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',1)) for i in xrange(s[0]): fid.write(struct.pack('d',float(matrix[i]))) #get to the "c" convention, hence the transpose else: - fid.write(struct.pack('i',s[0])) - fid.write(struct.pack('i',s[1])) + fid.write(struct.pack('i',s[0])) + fid.write(struct.pack('i',s[1])) for i in xrange(s[0]): for j in xrange(s[1]): @@ -363,16 +363,16 @@ #write length of record - fid.write(struct.pack('i',recordlength)) - - #write data code: - fid.write(struct.pack('i',FormatToCode(format))) + fid.write(struct.pack('i',recordlength)) + + #write data code: + fid.write(struct.pack('i',FormatToCode(format))) #now write length of string array - fid.write(struct.pack('i',len(data))) + fid.write(struct.pack('i',len(data))) #now write the strings for string in data: - fid.write(struct.pack('i',len(string))) - fid.write(struct.pack('%ds' % len(string),string)) + fid.write(struct.pack('i',len(string))) + fid.write(struct.pack('%ds' % len(string),string)) # }}} @@ -383,6 +383,6 @@ def FormatToCode(format): # {{{ """ - This routine takes the format string, and hardcodes it into an integer, which - is passed along the record, in order to identify the nature of the dataset being + This routine takes the format string, and hardcodes it into an integer, which + is passed along the record, in order to identify the nature of the dataset being sent. """