Revision 0461d2e117ce88704a56dd8bcbf6bf7787991b15 authored by Eh Tan on 08 November 2007, 23:28:46 UTC, committed by Eh Tan on 08 November 2007, 23:28:46 UTC
svn+ssh://svn@geodynamics.org/cig/mc/3D/CitcomS/trunk

........
  r8194 | tan2 | 2007-10-30 14:49:58 -0700 (Tue, 30 Oct 2007) | 1 line
  
  Compute d(rho)/dr/rho from rho(r)
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  r8195 | tan2 | 2007-10-30 14:50:52 -0700 (Tue, 30 Oct 2007) | 1 line
  
  Fixed a bug in dimensionalizing density. Provided the formula of geoid calculation in the comments. Rearranged the order of functions.
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  r8196 | tan2 | 2007-10-30 14:53:50 -0700 (Tue, 30 Oct 2007) | 1 line
  
  A post-processing program to project geoid coefficents onto a regular (longitude, latitude) mesh
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  r8197 | tan2 | 2007-10-30 14:54:14 -0700 (Tue, 30 Oct 2007) | 1 line
  
  Added the C program project_geoid to the makefile
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  r8199 | tan2 | 2007-10-30 15:29:44 -0700 (Tue, 30 Oct 2007) | 1 line
  
  Minor modification
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  r8201 | tan2 | 2007-11-01 16:33:30 -0700 (Thu, 01 Nov 2007) | 1 line
  
  Print dv/v=dp/p=1.0 for the 1st Uzawa iteraion
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  r8202 | tan2 | 2007-11-01 16:33:50 -0700 (Thu, 01 Nov 2007) | 1 line
  
  Fixed an error in comment
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  r8204 | tan2 | 2007-11-05 17:03:35 -0800 (Mon, 05 Nov 2007) | 1 line
  
  Scaled topo with variable gravity. Fixed an error in comment. Rearranged computation.
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  r8205 | tan2 | 2007-11-05 17:03:55 -0800 (Mon, 05 Nov 2007) | 1 line
  
  Removed functions related sph. harm in lib/Regional_obsolete.c
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  r8206 | tan2 | 2007-11-05 17:04:20 -0800 (Mon, 05 Nov 2007) | 1 line
  
  Shrank the size of sph. harm arrays
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  r8207 | tan2 | 2007-11-05 17:04:43 -0800 (Mon, 05 Nov 2007) | 1 line
  
  Init'd some variables about vtk_io, which might be accessed with uninit'd values in output_finalize()
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  r8212 | tan2 | 2007-11-06 15:17:54 -0800 (Tue, 06 Nov 2007) | 1 line
  
  Fixed a few memory errors
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  r8213 | tan2 | 2007-11-06 15:18:12 -0800 (Tue, 06 Nov 2007) | 1 line
  
  Increase vlowstep to match the default value in pyre
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  r8214 | tan2 | 2007-11-06 15:18:35 -0800 (Tue, 06 Nov 2007) | 1 line
  
  Removed unused multigrid parameters
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  r8215 | tan2 | 2007-11-06 15:18:54 -0800 (Tue, 06 Nov 2007) | 1 line
  
  Added cgrad solver convergence parameters, increased buoyancy_ratio and lower the # of steps
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  r8226 | tan2 | 2007-11-07 11:51:56 -0800 (Wed, 07 Nov 2007) | 1 line
  
  Print a warning when matrix eqn solver not converging
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  r8227 | tan2 | 2007-11-07 11:52:17 -0800 (Wed, 07 Nov 2007) | 1 line
  
  Removed comp_el from default output, since it is not required for restart anymore.
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  r8228 | tan2 | 2007-11-07 11:52:39 -0800 (Wed, 07 Nov 2007) | 1 line
  
  Decreased the # of processors. This is the only way I can reproduce single-cell convection as in the manual.
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  r8235 | tan2 | 2007-11-08 11:18:26 -0800 (Thu, 08 Nov 2007) | 1 line
  
  Dereased the timestep size to reduce artifacts in advection
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  r8236 | tan2 | 2007-11-08 11:18:52 -0800 (Thu, 08 Nov 2007) | 1 line
  
  Update NEWS
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  r8237 | tan2 | 2007-11-08 11:19:12 -0800 (Thu, 08 Nov 2007) | 1 line
  
  Update the version number
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  r8241 | tan2 | 2007-11-08 13:17:14 -0800 (Thu, 08 Nov 2007) | 1 line
  
  Updated file ChangeLog to r8240
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  r8242 | tan2 | 2007-11-08 13:36:55 -0800 (Thu, 08 Nov 2007) | 1 line
  
  Removed binary checkpoint files from makefile, as the file size is too big for distribution.
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  r8243 | tan2 | 2007-11-08 13:38:09 -0800 (Thu, 08 Nov 2007) | 1 line
  
  Updated file ChangeLog to r8242
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  r8244 | tan2 | 2007-11-08 14:31:21 -0800 (Thu, 08 Nov 2007) | 1 line
  
  Replaced a system call by std C library remove() and disabled another system call (backup input file). Partially fixed issue130. All remaining system calls are in lib/Output_gzdir.c.
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  r8245 | tan2 | 2007-11-08 14:41:31 -0800 (Thu, 08 Nov 2007) | 1 line
  
  Updated file ChangeLog to r8244
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Raw File
Solver.py
#!/usr/bin/env python
#
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
#<LicenseText>
#
# CitcomS.py by Eh Tan, Eun-seo Choi, and Pururav Thoutireddy.
# Copyright (C) 2002-2005, California Institute of Technology.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
#
#</LicenseText>
#
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#

from CitcomSLib import CPU_time, output, output_time, output_checkpoint, return_dt, return_t, return_step
from pyre.components.Component import Component
import journal



class Solver(Component):

    def __init__(self, name, facility="solver"):
        Component.__init__(self, name, facility)

        self.all_variables = None
        self.communicator = None
        self.start_cpu_time = 0
        return


    def _dt(self):
        '''get the value of dt from the C code'''
        return return_dt(self.all_variables)


    def _t(self):
        '''get the value of t from the C code'''
        return return_t(self.all_variables)


    def _step(self):
        '''get the value of step from the C code'''
        return return_step(self.all_variables)


    # Set these attributes as read-only properties, so that they are
    # always in accordance with their counterparts in the C code
    t = property(_t)
    dt = property(_dt)
    step = property(_step)


    def initialize(self, application):
        from CitcomSLib import citcom_init, global_default_values, set_signal

        comm = application.solverCommunicator
        all_variables = citcom_init(comm.handle())
        self.communicator = comm
        self.all_variables = all_variables

        self.initializeSolver()

        # information about clock time
        self.start_cpu_time = CPU_time()

        inv = self.inventory

        inv.mesher.initialize(all_variables)
        inv.tsolver.initialize(all_variables)
        inv.vsolver.initialize(all_variables)

        inv.bc.initialize(all_variables)
        inv.const.initialize(all_variables)
        inv.ic.initialize(all_variables)
        inv.output.initialize(all_variables)
        inv.param.initialize(all_variables)
        inv.phase.initialize(all_variables)
        inv.tracer.initialize(all_variables)
        inv.visc.initialize(all_variables)

        set_signal()
        global_default_values(self.all_variables)

        from CitcomSLib import return_rank, return_pid
        rank = return_rank(self.all_variables)
        if rank == 0:
            pid = return_pid(self.all_variables)
            stream = open("pid%d.cfg" % pid, "w")
        else:
            stream = None

        # XXX: This is a heck
        # Write controller inventory to pid file
        if stream:
            print >> stream, "[CitcomS.controller]"
            print >> stream, ("monitoringFrequency=%d" %
                application.controller.inventory.monitoringFrequency)
            print >> stream, ("checkpointFrequency=%d" %
                application.controller.inventory.checkpointFrequency)
            print >> stream

        self.setProperties(stream)

        self._setup()

        return


    def launch(self, application):
        if self.inventory.ic.inventory.restart:
            from CitcomSLib import readCheckpoint
            readCheckpoint(self.all_variables)

            # XXX: if post_processing
            # calling post_processing() and terminate
        else:
            # initial conditions
            ic = self.inventory.ic
            ic.launch()

            self.solveVelocities()
        return


    def _setup(self):
        mesher = self.inventory.mesher
        mesher.setup()

        vsolver = self.inventory.vsolver
        vsolver.setup()

        tsolver = self.inventory.tsolver
        tsolver.setup()

        # create mesh
        mesher.run()

        # initialize const. related to mesh
        vsolver.launch()
        tsolver.launch()
        return


    def solveVelocities(self):
        vsolver = self.inventory.vsolver
        vsolver.run()
        return



    def advectTemperature(self, dt):
        tsolver = self.inventory.tsolver
        tsolver.run(dt)
        return



    def advectTracers(self):
        self.inventory.tracer.run()
        return



    def newStep(self):
        return



    def stableTimestep(self):
        tsolver = self.inventory.tsolver
        dt = tsolver.stable_timestep()
        return dt



    def advance(self, dt):
        self.advectTemperature(dt)
        self.advectTracers()
        self.solveVelocities()
        return


    def endTimestep(self, done):
        self.inventory.visc.updateMaterial()
        self.inventory.bc.updatePlateVelocity()
        return done


    def endSimulation(self):
        self._avgCPUTime()
        self.finalize()
        return


    def _avgCPUTime(self):
        step = self.step
        total_cpu_time = CPU_time() - self.start_cpu_time

        rank = self.communicator.rank
        if not rank:
            import sys
            sys.stderr.write("Average cpu time taken for velocity step = %f\n"
                             % (total_cpu_time / (step+1)) )
        return


    def save(self, monitoringFrequency):
        step = self.step

        # output spacing is 'monitoringFrequency'
        if not (step % monitoringFrequency):
            output(self.all_variables, step)

        output_time(self.all_variables, step)
        return


    def checkpoint(self, checkpointFrequency):
        step = self.step

        if not (step % checkpointFrequency):
            output_checkpoint(self.all_variables)
        return


    def setProperties(self, stream):

        from CitcomSLib import Solver_set_properties

        Solver_set_properties(self.all_variables, self.inventory, stream)

        inv = self.inventory
        inv.mesher.setProperties(stream)
        inv.tsolver.setProperties(stream)
        inv.vsolver.setProperties(stream)

        inv.bc.setProperties(stream)
        inv.const.setProperties(stream)
        inv.ic.setProperties(stream)
        inv.output.setProperties(stream)
        inv.param.setProperties(stream)
        inv.phase.setProperties(stream)
        inv.tracer.setProperties(stream)
        inv.visc.setProperties(stream)

        return


    def finalize(self):
        from CitcomSLib import output_finalize
        output_finalize(self.all_variables)
        return


    class Inventory(Component.Inventory):

        import pyre.inventory as inv

        # component modules
        import CitcomS.Components.Advection_diffusion as Advection_diffusion
        import CitcomS.Components.Stokes_solver as Stokes_solver

        # components
        from CitcomS.Components.BC import BC
        from CitcomS.Components.Const import Const
        from CitcomS.Components.IC import IC
        from CitcomS.Components.Output import Output
        from CitcomS.Components.Param import Param
        from CitcomS.Components.Phase import Phase
        from CitcomS.Components.Tracer import Tracer
        from CitcomS.Components.Visc import Visc


        tsolver = inv.facility("tsolver",
                               factory=Advection_diffusion.temperature_diffadv)
        vsolver = inv.facility("vsolver",
                               factory=Stokes_solver.incompressibleNewtonian)

        bc = inv.facility("bc", factory=BC)
        const = inv.facility("const", factory=Const)
        ic = inv.facility("ic", factory=IC)
        output = inv.facility("output", factory=Output)
        param = inv.facility("param", factory=Param)
        phase = inv.facility("phase", factory=Phase)
        tracer = inv.facility("tracer", factory=Tracer)
        visc = inv.facility("visc", factory=Visc)

        datadir = inv.str("datadir", default=".")
        datadir_old = inv.str("datadir_old", default=".")

        rayleigh = inv.float("rayleigh", default=1e+05)
        dissipation_number = inv.float("dissipation_number", default=0.0)
        gruneisen = inv.float("gruneisen", default=0.0)
        surfaceT = inv.float("surfaceT", default=0.1)
        #adiabaticT0 = inv.float("adiabaticT0", default=0.4)
        Q0 = inv.float("Q0", default=0.0)

        stokes_flow_only = inv.bool("stokes_flow_only", default=False)

        verbose = inv.bool("verbose", default=False)
        see_convergence = inv.bool("see_convergence", default=True)


# version
__id__ = "$Id$"

# End of file
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