[cig-commits] [commit] master, python-removal, rajesh-petsc-schur: removed python versions of Cookbook parameter files (1fe296f)
cig_noreply at geodynamics.org
cig_noreply at geodynamics.org
Wed Nov 5 19:03:23 PST 2014
Repository : https://github.com/geodynamics/citcoms
On branches: master,python-removal,rajesh-petsc-schur
Link : https://github.com/geodynamics/citcoms/compare/464e1b32299b15819f93efd98d969cddb84dfe51...f97ae655a50bdbd6dac1923a3471ee4dae178fbd
>---------------------------------------------------------------
commit 1fe296f3453b9d10b4c7389cffb2dbb1a738cf0c
Author: Rajesh Kommu <rajesh.kommu at gmail.com>
Date: Wed Aug 27 12:52:37 2014 -0700
removed python versions of Cookbook parameter files
>---------------------------------------------------------------
1fe296f3453b9d10b4c7389cffb2dbb1a738cf0c
bin/pycitcoms.c | 108 ---------------------------------------
examples/Cookbook1/cookbook1.cfg | 18 -------
examples/Cookbook2/cookbook2.cfg | 37 --------------
examples/Cookbook3/cookbook3.cfg | 35 -------------
examples/Cookbook4/cookbook4.cfg | 48 -----------------
examples/Cookbook5/cookbook5.cfg | 54 --------------------
examples/Cookbook6/cookbook6.cfg | 85 ------------------------------
examples/Cookbook7/cookbook7.cfg | 69 -------------------------
examples/example0.cfg | 14 -----
examples/example1.cfg | 17 ------
10 files changed, 485 deletions(-)
diff --git a/bin/pycitcoms.c b/bin/pycitcoms.c
deleted file mode 100644
index 1fa59a7..0000000
--- a/bin/pycitcoms.c
+++ /dev/null
@@ -1,108 +0,0 @@
-/*
-//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-//
-//<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>
-//
-//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-#include <Python.h>
-#include <stddef.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <mpi.h>
-#include "CitcomSmodule.h"
-#ifdef WITH_EXCHANGER
-#include "Exchangermodule.h"
-#endif
-
-#define COMMAND \
-"import sys; " \
-"path = sys.argv[1]; " \
-"requires = sys.argv[2]; " \
-"entry = sys.argv[3]; " \
-"path = path.split(':'); " \
-"path.extend(sys.path); " \
-"sys.path = path; " \
-"from merlin import loadObject; " \
-"entry = loadObject(entry); " \
-"entry(sys.argv[3:], kwds={'requires': requires})"
-
-/* include the implementation of _mpi */
-#include "mpi/_mpi.c"
-
-struct _inittab inittab[] = {
- { "_mpi", init_mpi },
- { "CitcomSLib", initCitcomSLib },
-#ifdef WITH_EXCHANGER
- { "ExchangerLib", initExchangerLib },
-#endif
- { 0, 0 }
-};
-
-int main(int argc, char **argv)
-{
- int status;
-
-#ifdef USE_MPI
- /* initialize MPI */
- if (MPI_Init(&argc, &argv) != MPI_SUCCESS) {
- fprintf(stderr, "%s: MPI_Init failed! Exiting ...", argv[0]);
- return 1;
- }
-#endif
-
- /* add our extension module */
- if (PyImport_ExtendInittab(inittab) == -1) {
- fprintf(stderr, "%s: PyImport_ExtendInittab failed! Exiting...\n", argv[0]);
- return 1;
- }
-
- if (argc < 3 || strcmp(argv[1], "--pyre-start") != 0) {
- return Py_Main(argc, argv);
- }
-
- /* make sure 'sys.executable' is set to the path of this program */
- Py_SetProgramName(argv[0]);
-
- /* initialize Python */
- Py_Initialize();
-
- /* initialize sys.argv */
- PySys_SetArgv(argc - 1, argv + 1);
-
- /* run the Python command */
- status = PyRun_SimpleString(COMMAND) != 0;
-
- /* shut down Python */
- Py_Finalize();
-
-#ifdef USE_MPI
- /* shut down MPI */
- MPI_Finalize();
-#endif
-
- return status;
-}
-
-/* End of file */
diff --git a/examples/Cookbook1/cookbook1.cfg b/examples/Cookbook1/cookbook1.cfg
deleted file mode 100644
index f306ef4..0000000
--- a/examples/Cookbook1/cookbook1.cfg
+++ /dev/null
@@ -1,18 +0,0 @@
-# Cookbook 1: Global Model
-
-[CitcomS]
-solver = full
-steps = 100 ; number of time steps
-
-[CitcomS.controller]
-monitoringFrequency = 25 ; how often outputs are created
-
-[CitcomS.solver]
-datafile = cookbook1 ; prefix of output filenames
-
-[CitcomS.solver.ic]
-num_perturbations = 1
-perturbl = 3
-perturbm = 2
-perturblayer = 5
-perturbmag = 0.05
diff --git a/examples/Cookbook2/cookbook2.cfg b/examples/Cookbook2/cookbook2.cfg
deleted file mode 100644
index c8234f5..0000000
--- a/examples/Cookbook2/cookbook2.cfg
+++ /dev/null
@@ -1,37 +0,0 @@
-# Cookbook 2: Domain Size and Velocity Boundary Conditions
-
-[CitcomS]
-steps = 60 ; number of time steps
-
-[CitcomS.controller]
-monitoringFrequency = 30 ; how often outputs are created
-
-[CitcomS.solver]
-datafile = cookbook2 ; prefix of output filenames
-
-# Modify the layout of the mesh.
-[CitcomS.solver.mesher]
-nprocx = 2
-nprocy = 2
-nodex = 17
-nodey = 17
-nodez = 9
-
-theta_min = 0.7854
-theta_max = 1.5708
-fi_min = 0.0
-fi_max = 0.7854
-radius_inner = 0.55
-radius_outer = 1.0
-
-# Impose a uniform velocity across the top surface.
-[CitcomS.solver.bc]
-topvbc = 1
-topvbxval = 100
-topvbyval = 0
-
-# In addition, set the initial temperature perturbation to zero.
-[CitcomS.solver.ic]
-num_perturbations = 1
-perturbmag = 0.0
-
diff --git a/examples/Cookbook3/cookbook3.cfg b/examples/Cookbook3/cookbook3.cfg
deleted file mode 100644
index d03ebaa..0000000
--- a/examples/Cookbook3/cookbook3.cfg
+++ /dev/null
@@ -1,35 +0,0 @@
-# Cookbook 3: Temperature-dependent Viscosity
-
-[CitcomS]
-steps = 200 ; number of time steps
-
-[CitcomS.controller]
-monitoringFrequency = 25 ; how often outputs are created
-
-[CitcomS.solver]
-datafile = cookbook3 ; prefix of output filenames
-rayleigh = 1e6 ; Rayleigh number
-
-# Modify the layout of the mesh.
-[CitcomS.solver.mesher]
-nprocx = 2
-nprocy = 2
-nodex = 17
-nodey = 17
-nodez = 9
-
-# Assign the viscosities.
-[CitcomS.solver.visc]
-VISC_UPDATE = on
-num_mat = 4
-visc0 = 1,1,1,1
-TDEPV = on
-rheol = 4
-viscE = 0.2,0.2,0.2,0.2
-viscT = 0,0,0,0
-viscZ = 0,0,0,0
-VMIN = on
-visc_min = 1.0
-VMAX = on
-visc_max = 100.0
-
diff --git a/examples/Cookbook4/cookbook4.cfg b/examples/Cookbook4/cookbook4.cfg
deleted file mode 100644
index f8dc449..0000000
--- a/examples/Cookbook4/cookbook4.cfg
+++ /dev/null
@@ -1,48 +0,0 @@
-# Cookbook 4: Regionally Refined Meshes
-
-[CitcomS]
-steps = 250 ; number of time steps
-
-[CitcomS.controller]
-monitoringFrequency = 50 ; how often outputs are created
-
-[CitcomS.solver]
-rayleigh = 1e6 ; Rayleigh number
-datafile = cookbook4 ; prefix of output filenames
-
-[CitcomS.solver.ic]
-num_perturbations = 1
-perturbmag = 0.05
-perturblayer = 10
-
-# Perturb the initial temperature gradient in the longitudinal
-# direction.
-perturbl = 1
-perturbm = 0
-
-[CitcomS.solver.mesher]
-# Read uneven mesh point coordinates from 'coor.dat'.
-coor = 1
-coor_file = coor.dat
-
-nprocx = 1
-nprocy = 1
-nprocz = 1
-nodex = 33
-nodey = 17
-nodez = 17
-
-[CitcomS.solver.visc]
-VISC_UPDATE = on
-num_mat = 4
-visc0 = 1,1,1,1
-TDEPV = on
-rheol = 4
-viscE = 0.2,0.2,0.2,0.2
-viscT = 0,0,0,0
-viscZ = 0,0,0,0
-VMIN = on
-visc_min = 1.0
-VMAX = on
-visc_max = 100.0
-
diff --git a/examples/Cookbook5/cookbook5.cfg b/examples/Cookbook5/cookbook5.cfg
deleted file mode 100644
index 81592d6..0000000
--- a/examples/Cookbook5/cookbook5.cfg
+++ /dev/null
@@ -1,54 +0,0 @@
-# Cookbook 5: Subduction Models with Trench Rollback
-
-[CitcomS]
-steps = 1100 ; number of time steps
-
-[CitcomS.controller]
-monitoringFrequency = 100 ; how often outputs are created
-
-[CitcomS.solver]
-datafile = cookbook5
-datadir_old = ./ic
-datafile_old = cookbook5
-rayleigh = 4.07e+08
-
-[CitcomS.solver.bc]
-topvbc = 1
-
-[CitcomS.solver.param]
-file_vbcs = on
-start_age = 55
-
-# Since the starting age is set to 55 Ma, there will be 57 velocity
-# files, one for each Ma (bvel.dat0, bvel.dat1, ... bvel.dat56).
-vel_bound_file = ./velocity/bvel.dat
-
-[CitcomS.solver.ic]
-tic_method = -1
-solution_cycles_init = 0
-
-[CitcomS.solver.mesher]
-coor = 1
-coor_file = ./coor.dat
-nprocx = 1
-nprocy = 2
-nprocz = 1
-nodex = 17
-nodey = 65
-nodez = 33
-
-[CitcomS.solver.tsolver]
-finetunedt = 0.75
-monitor_max_T = on
-
-[CitcomS.solver.visc]
-num_mat = 4
-visc0 = 100,0.003,1,2
-TDEPV = on
-viscE = 24,24,24,24
-viscT = 0.182,0.182,0.182,0.182
-VMIN = on
-visc_min = 0.01
-VMAX = on
-visc_max = 100.0
-
diff --git a/examples/Cookbook6/cookbook6.cfg b/examples/Cookbook6/cookbook6.cfg
deleted file mode 100644
index 39a2d58..0000000
--- a/examples/Cookbook6/cookbook6.cfg
+++ /dev/null
@@ -1,85 +0,0 @@
-# Cookbook 6: Pseudo-Free-Surface Formulation
-
-[CitcomS]
-steps = 100
-
-
-[CitcomS.controller]
-monitoringFrequency = 10
-
-
-[CitcomS.solver]
-datafile = cookbook6
-rayleigh = 4.312616e+08
-
-
-[CitcomS.solver.mesher]
-nprocx = 2
-nprocy = 2
-nprocz = 1
-nodex = 61
-nodey = 61
-nodez = 25
-coor = 1
-coor_file = ./coord.dat
-
-
-[CitcomS.solver.tsolver]
-fixed_timestep = 7.77e-10
-
-
-[CitcomS.solver.vsolver]
-precond = on
-accuracy = 1e-5
-vlowstep = 100000
-piterations = 100000
-
-
-[CitcomS.solver.ic]
-# To try a different hot blob, one can specify three parameters:
-# 1. blob_center: Coordinates(theta,fi,r) of the center.
-# 2. blob_radius: Radius as non-dimensional distance.
-# 3. blob_dT: The amount of temperature increase/decrease
-# within the blob as non-dimensional temperature.
-#
-# Note: It is required to keep "tic_method = 2" to have the initial
-# hot blob.
-tic_method = 2
-blob_center = 1.570800e+00,1.570800e+00,9.246600e-01
-blob_radius = 6.278334e-02
-blob_dT = 0.18
-half_space_age = 2500.0
-mantle_temp = 0.82
-
-
-[CitcomS.solver.bc]
-topvbc = 2
-pseudo_free_surf = on
-bottbcval = 0.82
-
-# To convert pseudo-free-surface B.C. to free-slip B.C., do the
-# following:
-
-#topvbc = 0
-#pseudo_free_surf = off
-
-
-[CitcomS.solver.param]
-start_age = 60
-
-
-[CitcomS.solver.visc]
-TDEPV = on
-visc0 = 1,1,1,1
-viscE = 9.50614,9.50614,9.50614,9.50614
-viscT = 1.02126,1.02126,1.02126,1.02126
-
-
-[CitcomS.solver.const]
-radius = 6.371e+06
-density = 3270.0
-thermdiff = 1.0e-06
-gravacc = 10.0
-thermexp = 3.0e-05
-refvisc = 1.0e+21
-
diff --git a/examples/Cookbook7/cookbook7.cfg b/examples/Cookbook7/cookbook7.cfg
deleted file mode 100644
index 73bbad4..0000000
--- a/examples/Cookbook7/cookbook7.cfg
+++ /dev/null
@@ -1,69 +0,0 @@
-# Cookbook 7: Global Thermo-chemical Convection Model
-
-[CitcomS]
-solver = full
-steps = 15 ; number of time steps
-
-
-[CitcomS.controller]
-monitoringFrequency = 5 ; how often outputs are created
-
-
-[CitcomS.solver]
-datadir = output ; path to output directory
-datafile = cookbook7 ; prefix of output filenames
-rayleigh = 1e7
-
-
-[CitcomS.solver.ic]
-num_perturbations = 1
-perturbl = 3
-perturbm = 2
-perturblayer = 5
-perturbmag = 0.05
-
-
-[CitcomS.solver.output]
-output_optional = tracer,comp_nd
-
-
-[CitcomS.solver.tracer]
-tracer = on
-tracer_ic_method = 0
-tracers_per_element = 20
-tracer_file = tracer.dat
-
-tracer_flavors = 2
-ic_method_for_flavors = 0
-z_interface = 0.7
-
-chemical_buoyancy = 1
-buoy_type = 1
-buoyancy_ratio = 0.5
-
-regular_grid_deltheta = 1.0
-regular_grid_delphi = 1.0
-
-
-[CitcomS.solver.vsolver]
-Solver = cgrad
-accuracy = 1e-04
-vlowstep = 1000
-piterations = 1000
-
-
-# Assign the viscosities.
-[CitcomS.solver.visc]
-VISC_UPDATE = on
-num_mat = 4
-visc0 = 1,1,1,1
-TDEPV = on
-rheol = 4
-viscE = 0.2,0.2,0.2,0.2
-viscT = 0,0,0,0
-viscZ = 0,0,0,0
-VMIN = on
-visc_min = 1.0
-VMAX = on
-visc_max = 100.0
-
diff --git a/examples/example0.cfg b/examples/example0.cfg
deleted file mode 100644
index d0db18d..0000000
--- a/examples/example0.cfg
+++ /dev/null
@@ -1,14 +0,0 @@
-
-[CitcomS]
-steps = 5
-
-[CitcomS.controller]
-monitoringFrequency = 1
-
-[CitcomS.solver]
-datafile = example0
-
-[CitcomS.solver.mesher]
-nodex = 17
-nodey = 17
-
diff --git a/examples/example1.cfg b/examples/example1.cfg
deleted file mode 100644
index 6f84375..0000000
--- a/examples/example1.cfg
+++ /dev/null
@@ -1,17 +0,0 @@
-
-[CitcomS]
-steps = 70
-
-[CitcomS.controller]
-monitoringFrequency = 10
-
-[CitcomS.solver]
-datafile = example1
-
-[CitcomS.solver.mesher]
-nprocx = 2
-nprocy = 2
-nodex = 17
-nodey = 17
-nodez = 9
-
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