Merge pull request #10 from VirtualPlanetaryLaboratory/dev

updated documentation and re-added bp functionality

docs/help.rst

@@ -1,27 +1,28 @@
-Running multi-planet
+Running MultiPlanet
 ====================
 
-To run :code:`multi-planet` on a large number of simulations, first run 
-:code:`vspace` to create the simulation folders. Then, in that same directory, type:
+To run :code:`MultiPlanet` on a large number of simulations, first run :code:`VSPACE` to
+create the simulation folders. Then, in that same directory, type:
 
 .. code-block:: bash
 
-    multi-planet <input file> -c [number of cores] -q -bp -m [email]
+    multiplanet <input file> -c [number of cores] -q -bp -m [email]
 
-Where the "input file" **must be the same file** used with :code:`vspace`. You can
+Where the "input file" **must be the same file** used with :code:`VSPACE`. You can
 specify the number of cores, but the default is the maximum number of cores.
 
-There are three optional arguments for ``multi-planet``:
+There are three optional arguments for ``MultiPlanet``:
 
 :code:`-q`: there will be no output in the command line
 
-:code:`-bp`: `bigplanet`_ will be ran in after ``multi-planet``.
+ :code:`-bp`: `BigPlanet`_ will be ran in conjunction with MultiPlanet.
 
-.. _bigplanet: https://github.com/VirtualPlanetaryLaboratory/bigplanet
+ .. BigPlanet: https://github.com/VirtualPlanetaryLaboratory/bigplanet
 
 :code:`-m`: emails the users at :code:`email` when the simulations are complete
 
-``multi-planet`` keeps track of the status of the parameter sweep. Should the run halt 
-early for any reason,  simply run ``multi-planet`` again it will restart all the simulations
+
+``MultiPlanet`` keeps track of the status of the parameter sweep. Should the run halt 
+early for any reason,  simply run ``MultiPlanet`` again it will restart all the simulations
 that crashed and continue on with the parameter sweep. You can also check the status
 of the parameter sweep with `mpstatus <mpstatus>`_.

docs/index.rst

@@ -1,13 +1,11 @@
-multi-planet Documentation
-==========================
+MultiPlanet Documentation
+=======
 
 ``multi-planet`` manages the exectution of a suite of `VPLanet <https://github.com/VirtualPlanetaryLaboratory/multi-planet>`_
 simulations that were built with `VSPACE <https://github.com/VirtualPlanetaryLaboratory/vspace>`_. 
 ``multi-planet`` performs simulations across multi-core computers and can be used to restart jobs that fail for any reason.
 This repository also includes ``mpstatus``, which returns the current status of the parameter sweep.
 
-
-
 .. toctree::
    :maxdepth: 1
 
@@ -18,7 +16,8 @@ This repository also includes ``mpstatus``, which returns the current status of
 
 .. note::
 
-    To maximize ``multi-planet``'s power, run ``vspace`` and ``mulit-planet -bp`` to automatically
-    build a bigplanet archive immediately after the simulations finish.  Then create 
-    bigplanet files from the archive as needed, and use ``bigplanet``'s scripting functions to 
+    To maximize MultiPlanet's power, run ``VSPACE`` with the ``-bp`` option to automatically
+    build the [`BigPlanet`](https://github.com/VirtualPlanetaryLaboratory/bigplanet) archive 
+    immediately after the simulations finish.  Then create  BigPlanet files from the 
+    archive as needed, and use ``BigPlanet``'s scripting functions to 
     extract vectors and matrices for plotting, statistical analyses, etc.

docs/install.rst

@@ -1,30 +1,28 @@
 Installation Guide
 ==================
 
-There are two ways to install ``multi-planet``: 1) in conjunction with 
+There are two ways to install ``MultiPlanet``: 1) in conjunction with 
 `VPLanet <https://github.com/VirtualPlanetaryLaboratory/vplanet>`_ and 
 its other support scripts, or 2) from source.
 
-To install bigplanet and the other ``VPLanet`` packages, use the command:
+To install MultiPlanet and the other ``VPLanet`` packages, use the command:
 
 .. code-block:: bash
 
     python -m pip install vplanet
 
 To install from source, first close the repo:
 
-
 .. code-block:: bash
 
     git clone https://github.com/VirtualPlanetaryLaboratory/multi-planet.git
 
-and then go into the directory (bigplanet) and run the setup script:
+and then go into the directory (MultiPlanet) and run the setup script:
 
 .. code-block:: bash
 
-    cd multi-planet
+    cd multi-planet/
     python setup.py install
 
-
-The setup script installs the various dependencies, creates the ``multi-planet`` and ``mpstatus``
+The setup script installs the various dependencies, creates the ``MultiPlanet`` and ``mpstatus``
 executables, and adds them to your PATH. 

docs/mpstatus.rst

@@ -1,18 +1,18 @@
-Status Reports
-==============
+Checking the status of the MultiPlanet Simulations
+===================================================
 
 To check the status of your simulations, type
 
 .. code-block:: bash
 
     mpstatus <input file>
 
-where the *input file* **must be the same file** used with :code:`vspace` and 
-:code:`multi-planet`. The following will be printed to the command line:
+where the "input file" **must be the same file** used with :code:`VSPACE` and :code:`MultiPlanet`.
+The following will be printed to the command line:
 
 .. code-block:: bash
 
-    --Multi-Planet Status--
+    --MultiPlanet Status--
     Number of Simulations completed: 10
     Number of Simulations in progress: 5
     Number of Simulations remaining: 20

multiplanet/multiplanet.py

@@ -5,8 +5,8 @@
 import argparse
 import h5py
 import numpy as np
-#from bigplanet import *
-#Sfrom bigplanet.bp_process import GatherData,DictToBP
+from bigplanet.bp_get import GetVplanetHelp
+from bigplanet.bp_process import GatherData,DictToBP
 
 # --------------------------------------------------------------------
 
@@ -160,10 +160,9 @@ def par_worker(checkpoint_file,system_name,body_list,log_file,in_files,verbose,l
 
         lock.acquire()
         datalist = []
-        bigplanet == False
-        #if bigplanet == True:
-            #data = {}
-            #vplanet_help = GetVplanetHelp()
+        if bigplanet == True:
+            data = {}
+            vplanet_help = GetVplanetHelp()
 
         with open(checkpoint_file, "r") as f:
             for newline in f:
@@ -220,14 +219,14 @@ def par_worker(checkpoint_file,system_name,body_list,log_file,in_files,verbose,l
                     break
             if verbose:
                 print(folder, "completed")
-            # if bigplanet == True:
-            #     with h5py.File(h5_file, "a") as Master:
-            #         group_name = folder.split("/")[-1]
-            #         if group_name not in Master:
-            #             data = GatherData(data, system_name, body_list,
-            #                               log_file, in_files, vplanet_help, folder, verbose)
-            #             DictToBP(data, vplanet_help, Master,
-            #                      verbose, group_name, archive=True)
+            if bigplanet == True:
+                with h5py.File(h5_file, "a") as Master:
+                    group_name = folder.split("/")[-1]
+                    if group_name not in Master:
+                        data = GatherData(data, system_name, body_list,
+                                          log_file, in_files, vplanet_help, folder, verbose)
+                        DictToBP(data, vplanet_help, Master,
+                                 verbose, group_name, archive=True)
         else:
             for l in datalist:
                 if l[0] == folder:

tests/Bigplanet/bpl.in

@@ -0,0 +1,9 @@
+sDestFolder MP_Bigplanet
+sArchiveFile MP_Bigplanet.bpa
+
+saBodyFiles earth.in venus.in sun.in
+
+sPrimaryFile vpl.in
+
+
+

tests/Bigplanet/earth.in

@@ -0,0 +1,55 @@
+# Earthlike parameters
+sName		earth			# Body's name
+saModules 	radheat thermint
+
+# Physical Properties
+dMass		-1.0  			# Mass, negative -> Earth masses
+dRadius		-1.0  			# Radius, negative -> Earth radii
+dRotPeriod	-1.0  			# Rotation period, negative -> days
+dObliquity	23.5
+dRadGyra	0.5
+# Orbital Properties
+dEcc            0.0167		# Eccentricity
+dSemi           -1		# Semi-major axis, negative -> AU
+
+
+# RADHEAT Parameters
+# *Num* are in numbers of atoms, negative -> Earth vals
+### 40K
+d40KPowerMan      -1
+d40KPowerCore     -1
+d40KPowerCrust    -1
+### 232Th
+d232ThPowerMan	  -1
+d232ThPowerCore	  -1
+d232ThPowerCrust  -1
+### 235U
+d235UPowerMan     -1
+d235UPowerCore	  -1
+d235UPowerCrust	  -1
+### 238U
+d238UPowerMan	  -1
+d238UPowerCore	  -1
+d238UPowerCrust	  -1
+
+### THERMINT inputs.
+dTMan          3000
+dTCore         6000
+#dViscJumpMan     2.40
+
+saOutputOrder -Time -TMan -TUMan -TLMan -TCMB -TCore $
+    -HflowUMan -HflowMeltMan -RadPowerMan -RadPowerCore -RadPowerCrust $
+    -HflowCMB -HflowSecMan $
+    -TDotMan -TDotCore -TJumpLMan -TJumpUMan -RIC -RayleighMan -ViscUMan -ViscLMan $
+    -MeltMassFluxMan -FMeltUMan $
+    -MagMom -CoreBuoyTherm -CoreBuoyCompo -CoreBuoyTotal -MagPauseRad $
+    -BLUMan -BLLMan $
+    -238UPowerMan -238UNumMan -238UMassMan -238UPowerCore -238UNumCore -238UMassCore $
+    -238UPowerCrust -238UNumCrust -238UMassCrust $
+    -235UPowerMan -235UNumMan -235UMassMan -235UPowerCore -235UNumCore -235UMassCore $
+    -235UPowerCrust -235UNumCrust -235UMassCrust $
+    -232ThPowerMan -232ThNumMan -232ThMassMan -232ThPowerCore -232ThNumCore -232ThMassCore $
+    -232ThPowerCrust -232ThNumCrust -232ThMassCrust $
+    -40KPowerMan -40KNumMan -40KMassMan -40KPowerCore -40KNumCore -40KMassCore $
+    -40KPowerCrust -40KNumCrust -40KMassCrust ChiOC ChiIC MassChiOC MassChiIC MassOC MassIC $
+    -RadPowerTotal

tests/Bigplanet/sun.in

@@ -0,0 +1,9 @@
+# sun parameters
+sName        sun
+dMass        1
+dSemi        0
+dEcc         0
+dRadius      0.00135
+dLuminosity  3.846e26
+sStellarModel none
+saModules    stellar

tests/Bigplanet/test_bigplanet.py

@@ -0,0 +1,32 @@
+import subprocess
+import numpy as np
+import os
+import pathlib
+import multiprocessing as mp
+import warnings
+import sys
+
+def test_mp_bigplanet():
+    #gets current path
+    path = pathlib.Path(__file__).parents[0].absolute()
+    sys.path.insert(1, str(path.parents[0]))
+
+    #gets the number of cores on the machine
+    cores = mp.cpu_count()
+    if cores == 1:
+        warnings.warn("There is only 1 core on the machine",stacklevel=3)
+    else:
+        # Run vspace
+        if not (path / "MP_Bigplanet").exists():
+            subprocess.check_output(["vspace", "vspace.in"], cwd=path)
+
+        # Run multi-planet
+        if not (path / ".MP_Bigplanet").exists():
+            subprocess.check_output(["multiplanet", "vspace.in", "-bp"], cwd=path)
+
+        file = path / "MP_Bigplanet.bpa"
+
+        assert os.path.isfile(file) == True
+
+if __name__ == "__main__":
+    test_mp_bigplanet()

tests/Bigplanet/vpl.in

@@ -0,0 +1,44 @@
+# Example primary input file for VPLANET
+sSystemName	earth			# System Name
+iVerbose	5			# Verbosity level
+bOverwrite	1			# Allow file overwrites?
+
+# All space after a # is ignored, as is white space
+# The first lowercase letter(s) denote the cast: b=boolean, i=int, d=double,
+# s=string. An "a" indicates an array and multiple arguments are allowed/expected.
+
+# List of "body files" that contain body-specific parameters
+saBodyFiles	sun.in $	# The host star
+		earth.in	# Earth
+
+
+# Array options can continue to the next line with a terminating "$". The $ can be
+# at the end of the string or not. Comments are allowed afterwards.
+
+# Input/Output Units
+sUnitMass	solar		# Options: gram, kg, Earth, Neptune, Jupiter, solar
+sUnitLength	aU		# Options: cm, m, km, Earth, Jupiter, solar, AU
+sUnitTime	YEARS		# Options: sec, day, year, Myr, Gyr
+sUnitAngle	d		# Options: deg, rad
+sUnitTemp       K
+
+# Units specified in the primary input file are propagated into the bodies. Otherwise
+# specifiy units on a per body basis in the body files.
+# Most string arguments can be in any case and need only be unambiguous.
+
+# Input/Output
+bDoLog		1		# Write a log file?
+iDigits		6		# Maximum number of digits to right of decimal
+dMinValue	1e-10		# Minimum value of eccentricity/obliquity
+
+# Option names must be exact in spelling and case.
+
+# Evolution Parameters
+bDoForward	1		# Perform a forward evolution?
+bVarDt		1		# Use variable timestepping?
+dEta		0.1		# Coefficient for variable timestepping
+dStopTime	4.5e9  #1e10		# Stop time for evolution
+dOutputTime	1e7  # 4.5e9		# Output timesteps (assuming in body files)
+
+# Some options are only permitted in the primary file, some are forbidden.
+# That should really be documented!

tests/Bigplanet/vspace.in

@@ -0,0 +1,10 @@
+sSrcFolder  .
+sDestFolder MP_Bigplanet
+sTrialName  semi_
+
+sBodyFile   earth.in
+dSemi [1, 2, n3] a
+
+sBodyFile sun.in
+
+sPrimaryFile vpl.in