From 95cdbdc90c9d1d2e20da70c7623f19cec728b250 Mon Sep 17 00:00:00 2001
From: Johanna Huck <jobst@berkeley.edu>
Date: Tue, 26 May 2015 21:57:27 -0700
Subject: [PATCH 01/20] start dftplots examples

---
 ccsgp_get_started/dftplots/README.md | 3 +++
 1 file changed, 3 insertions(+)
 create mode 100644 ccsgp_get_started/dftplots/README.md

diff --git a/ccsgp_get_started/dftplots/README.md b/ccsgp_get_started/dftplots/README.md
new file mode 100644
index 0000000..92e88db
--- /dev/null
+++ b/ccsgp_get_started/dftplots/README.md
@@ -0,0 +1,3 @@
+### DFTplots
+
+scripts to generate plots for DFT benchmarking paper 

From 28cbd44f43e3f527ec4b6a7a7d861c29e21e2013 Mon Sep 17 00:00:00 2001
From: Johanna Huck <jobst@berkeley.edu>
Date: Tue, 16 Jun 2015 16:13:19 -0700
Subject: [PATCH 02/20] initial commit for dftplots

---
 ccsgp_get_started/dftplots/__init__.py      |  0
 ccsgp_get_started/dftplots/gp_bindenergy.py | 87 +++++++++++++++++++++
 2 files changed, 87 insertions(+)
 create mode 100644 ccsgp_get_started/dftplots/__init__.py
 create mode 100644 ccsgp_get_started/dftplots/gp_bindenergy.py

diff --git a/ccsgp_get_started/dftplots/__init__.py b/ccsgp_get_started/dftplots/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/ccsgp_get_started/dftplots/gp_bindenergy.py b/ccsgp_get_started/dftplots/gp_bindenergy.py
new file mode 100644
index 0000000..4080056
--- /dev/null
+++ b/ccsgp_get_started/dftplots/gp_bindenergy.py
@@ -0,0 +1,87 @@
+import logging, argparse, os, sys
+import numpy as np
+from collections import OrderedDict
+from ..ccsgp.ccsgp import make_plot
+from ..examples.utils import getWorkDirs
+from ..ccsgp.utils import getOpts
+
+def gp_bindenergy(guest):
+  """example for plotting from a text file via numpy.loadtxt
+
+  1. prepare input/output directories
+  2. load the data into an OrderedDict() [adjust axes units]
+  3. sort countries from highest to lowest population
+  4. select the <topN> most populated countries
+  5. call ccsgp.make_plot with data from 4
+
+  Below is an output image for country initial T and the 4 most populated
+  countries for this initial (click to enlarge). Also see::
+
+    $ python -m ccsgp_get_started.examples.gp_datdir -h
+
+  for help on the command line options.
+
+  .. image:: pics/T.png
+     :width: 450 px
+
+  .. image:: pics/U.png
+     :width: 450 px
+
+  :param initial: country initial
+  :type initial: str
+  :param topN: number of most populated countries to plot
+  :type topN: int
+  :ivar inDir: input directory according to package structure and initial
+  :ivar outDir: output directory according to package structure
+  :ivar data: OrderedDict with datasets to plot as separate keys
+  :ivar file: data input file for specific country, format: [x y] OR [x y dx dy]
+  :ivar country: country, filename stem of input file
+  :ivar file_url: absolute url to input file
+  :ivar nSets: number of datasets
+  """
+  # prepare input/output directories
+  inDir, outDir = getWorkDirs()
+  guest = guest.capitalize()
+  inDir = os.path.join(inDir, guest)
+  if not os.path.exists(inDir): # catch missing initial
+    return "guest %s doesn't exist" % guest
+  # prepare data
+  data = OrderedDict()
+  for file in os.listdir(inDir):
+    funct = os.path.splitext(file)[0]
+    file_url = os.path.join(inDir, file)
+    data[funct] = np.loadtxt(open(file_url, 'rb')) # load data
+    if data[funct].shape[1] > 2: data[funct][:, 3:] /= 1e6
+  logging.debug(data) # shown if --log flag given on command line
+  # sort countries according to mean population (highest -> lowest)
+  sorted_data = OrderedDict(sorted(
+    data.items(), key = lambda t: np.mean(t[1][:,1]), reverse = True
+  ))
+ # # "pop" (select) N most populated countries
+ # top_data = OrderedDict(
+ #   sorted_data.popitem(last = False) for i in xrange(topN)
+ #   if sorted_data
+ # )
+  # generate plot using ccsgp.make_plot
+  nSets = len(data)
+  make_plot(
+    data = data.values(),
+    properties = [ getOpts(i) for i in xrange(nSets) ],
+    titles = data.keys(), # use data keys as legend titles
+    name = os.path.join(outDir, guest),
+    key = [ 'at graph 1., 1.2', 'maxrows 2' ],
+    ylabel = 'binding energy (kJ/mol)',
+    xlabel = 'metals', rmargin = 0.99, tmargin = 0.85, size='8.5in,8in'
+  )
+  return 'done'
+
+if __name__ == '__main__':
+  parser = argparse.ArgumentParser()
+  parser.add_argument("guest", help="guest = input subdir with txt files")
+  parser.add_argument("--log", help="show log output", action="store_true")
+  args = parser.parse_args()
+  loglevel = 'DEBUG' if args.log else 'WARNING'
+  logging.basicConfig(
+    format='%(message)s', level=getattr(logging, loglevel)
+  )
+  print gp_bindenergy(args.guest)

From 64a1023452387738fb8a172bbbd044b9819ec465 Mon Sep 17 00:00:00 2001
From: Johanna Huck <jobst@berkeley.edu>
Date: Tue, 16 Jun 2015 16:28:16 -0700
Subject: [PATCH 03/20] delete all gp_datadir leftover defs

---
 ccsgp_get_started/dftplots/gp_bindenergy.py | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/ccsgp_get_started/dftplots/gp_bindenergy.py b/ccsgp_get_started/dftplots/gp_bindenergy.py
index 4080056..b1bbae0 100644
--- a/ccsgp_get_started/dftplots/gp_bindenergy.py
+++ b/ccsgp_get_started/dftplots/gp_bindenergy.py
@@ -51,17 +51,7 @@ def gp_bindenergy(guest):
     funct = os.path.splitext(file)[0]
     file_url = os.path.join(inDir, file)
     data[funct] = np.loadtxt(open(file_url, 'rb')) # load data
-    if data[funct].shape[1] > 2: data[funct][:, 3:] /= 1e6
   logging.debug(data) # shown if --log flag given on command line
-  # sort countries according to mean population (highest -> lowest)
-  sorted_data = OrderedDict(sorted(
-    data.items(), key = lambda t: np.mean(t[1][:,1]), reverse = True
-  ))
- # # "pop" (select) N most populated countries
- # top_data = OrderedDict(
- #   sorted_data.popitem(last = False) for i in xrange(topN)
- #   if sorted_data
- # )
   # generate plot using ccsgp.make_plot
   nSets = len(data)
   make_plot(

From 3b01f97c980f9618954e1ccfd35b71f73dace583 Mon Sep 17 00:00:00 2001
From: Johanna Huck <jobst@berkeley.edu>
Date: Tue, 16 Jun 2015 16:45:02 -0700
Subject: [PATCH 04/20] update pydocs to match script

---
 ccsgp_get_started/dftplots/gp_bindenergy.py | 23 ++++++---------------
 1 file changed, 6 insertions(+), 17 deletions(-)

diff --git a/ccsgp_get_started/dftplots/gp_bindenergy.py b/ccsgp_get_started/dftplots/gp_bindenergy.py
index b1bbae0..3e9a360 100644
--- a/ccsgp_get_started/dftplots/gp_bindenergy.py
+++ b/ccsgp_get_started/dftplots/gp_bindenergy.py
@@ -10,32 +10,21 @@ def gp_bindenergy(guest):
 
   1. prepare input/output directories
   2. load the data into an OrderedDict() [adjust axes units]
-  3. sort countries from highest to lowest population
-  4. select the <topN> most populated countries
-  5. call ccsgp.make_plot with data from 4
+  3. call ccsgp.make_plot with data from 4
 
-  Below is an output image for country initial T and the 4 most populated
-  countries for this initial (click to enlarge). Also see::
+  Also see::
 
-    $ python -m ccsgp_get_started.examples.gp_datdir -h
+    $ python -m ccsgp_get_started.dftplots.gp_bindenergy -h
 
   for help on the command line options.
 
-  .. image:: pics/T.png
-     :width: 450 px
-
-  .. image:: pics/U.png
-     :width: 450 px
-
-  :param initial: country initial
-  :type initial: str
-  :param topN: number of most populated countries to plot
-  :type topN: int
+  :param guest: guest molecule
+  :type guest: str
   :ivar inDir: input directory according to package structure and initial
   :ivar outDir: output directory according to package structure
   :ivar data: OrderedDict with datasets to plot as separate keys
   :ivar file: data input file for specific country, format: [x y] OR [x y dx dy]
-  :ivar country: country, filename stem of input file
+  :ivar funct: functional, filename stem of input file
   :ivar file_url: absolute url to input file
   :ivar nSets: number of datasets
   """

From bf349774338dcfbf24154ec51065ec6bae57390a Mon Sep 17 00:00:00 2001
From: Johanna Huck <jobst@berkeley.edu>
Date: Tue, 16 Jun 2015 16:56:04 -0700
Subject: [PATCH 05/20] 2. update pydocs to match script

---
 ccsgp_get_started/dftplots/gp_bindenergy.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/ccsgp_get_started/dftplots/gp_bindenergy.py b/ccsgp_get_started/dftplots/gp_bindenergy.py
index 3e9a360..c424040 100644
--- a/ccsgp_get_started/dftplots/gp_bindenergy.py
+++ b/ccsgp_get_started/dftplots/gp_bindenergy.py
@@ -10,7 +10,7 @@ def gp_bindenergy(guest):
 
   1. prepare input/output directories
   2. load the data into an OrderedDict() [adjust axes units]
-  3. call ccsgp.make_plot with data from 4
+  3. call ccsgp.make_plot with data from 2
 
   Also see::
 
@@ -20,19 +20,18 @@ def gp_bindenergy(guest):
 
   :param guest: guest molecule
   :type guest: str
-  :ivar inDir: input directory according to package structure and initial
+  :ivar inDir: input directory according to package structure and guest
   :ivar outDir: output directory according to package structure
   :ivar data: OrderedDict with datasets to plot as separate keys
-  :ivar file: data input file for specific country, format: [x y] OR [x y dx dy]
+  :ivar file: data input file for specific guest, format: [x y] OR [x y dx dy]
   :ivar funct: functional, filename stem of input file
   :ivar file_url: absolute url to input file
   :ivar nSets: number of datasets
   """
   # prepare input/output directories
   inDir, outDir = getWorkDirs()
-  guest = guest.capitalize()
   inDir = os.path.join(inDir, guest)
-  if not os.path.exists(inDir): # catch missing initial
+  if not os.path.exists(inDir): # catch missing guest
     return "guest %s doesn't exist" % guest
   # prepare data
   data = OrderedDict()

From 41b818e356e415b9d043d413fe5d34842a57329c Mon Sep 17 00:00:00 2001
From: Johanna Huck <jobst@berkeley.edu>
Date: Wed, 17 Jun 2015 16:21:43 -0700
Subject: [PATCH 06/20] include bars, boxwidth and color fill

---
 ccsgp_get_started/dftplots/gp_bindenergy.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/ccsgp_get_started/dftplots/gp_bindenergy.py b/ccsgp_get_started/dftplots/gp_bindenergy.py
index c424040..ac12443 100644
--- a/ccsgp_get_started/dftplots/gp_bindenergy.py
+++ b/ccsgp_get_started/dftplots/gp_bindenergy.py
@@ -4,6 +4,7 @@
 from ..ccsgp.ccsgp import make_plot
 from ..examples.utils import getWorkDirs
 from ..ccsgp.utils import getOpts
+from ..ccsgp.config import default_colors
 
 def gp_bindenergy(guest):
   """example for plotting from a text file via numpy.loadtxt
@@ -44,12 +45,14 @@ def gp_bindenergy(guest):
   nSets = len(data)
   make_plot(
     data = data.values(),
-    properties = [ getOpts(i) for i in xrange(nSets) ],
+    properties = [ 'with boxes lc %s' % (default_colors[1])],
+    gpcalls = [ 'boxwidth 0.2 absolute', 'style fill solid 1.0 border lt -1'],
     titles = data.keys(), # use data keys as legend titles
     name = os.path.join(outDir, guest),
     key = [ 'at graph 1., 1.2', 'maxrows 2' ],
     ylabel = 'binding energy (kJ/mol)',
-    xlabel = 'metals', rmargin = 0.99, tmargin = 0.85, size='8.5in,8in'
+    xlabel = 'metals', rmargin = 0.99, tmargin = 0.85, size='8.5in,8in',
+    debug = True
   )
   return 'done'
 

From 3fa9fb68b8bcdf0a50ef587ed17cced26444e46a Mon Sep 17 00:00:00 2001
From: Johanna Huck <jobst@berkeley.edu>
Date: Tue, 23 Jun 2015 16:18:35 -0700
Subject: [PATCH 07/20] plot set in diff. colored bars & change xtics to match
 metal

---
 ccsgp_get_started/dftplots/gp_bindenergy.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/ccsgp_get_started/dftplots/gp_bindenergy.py b/ccsgp_get_started/dftplots/gp_bindenergy.py
index ac12443..763f3a2 100644
--- a/ccsgp_get_started/dftplots/gp_bindenergy.py
+++ b/ccsgp_get_started/dftplots/gp_bindenergy.py
@@ -45,8 +45,10 @@ def gp_bindenergy(guest):
   nSets = len(data)
   make_plot(
     data = data.values(),
-    properties = [ 'with boxes lc %s' % (default_colors[1])],
-    gpcalls = [ 'boxwidth 0.2 absolute', 'style fill solid 1.0 border lt -1'],
+    properties = [ 'with boxes lc %s' % (default_colors[i]) for i in
+                                         range(nSets)],
+    gpcalls = [ 'boxwidth 0.2 absolute', 'style fill solid 1.0 border lt 0',
+               'xtics ("Mg"1, "Mn"2, "Fe"3, "Co"4, "Ni"5, "Cu"6, "Zn"7)'],
     titles = data.keys(), # use data keys as legend titles
     name = os.path.join(outDir, guest),
     key = [ 'at graph 1., 1.2', 'maxrows 2' ],

From 2bb2e3d4f8d450a6a33ef1c5de163abf40d0300b Mon Sep 17 00:00:00 2001
From: Johanna Huck <jobst@berkeley.edu>
Date: Tue, 23 Jun 2015 16:19:13 -0700
Subject: [PATCH 08/20] change size of key to fit funct. names

---
 ccsgp_get_started/dftplots/gp_bindenergy.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ccsgp_get_started/dftplots/gp_bindenergy.py b/ccsgp_get_started/dftplots/gp_bindenergy.py
index 763f3a2..040d06f 100644
--- a/ccsgp_get_started/dftplots/gp_bindenergy.py
+++ b/ccsgp_get_started/dftplots/gp_bindenergy.py
@@ -51,7 +51,7 @@ def gp_bindenergy(guest):
                'xtics ("Mg"1, "Mn"2, "Fe"3, "Co"4, "Ni"5, "Cu"6, "Zn"7)'],
     titles = data.keys(), # use data keys as legend titles
     name = os.path.join(outDir, guest),
-    key = [ 'at graph 1., 1.2', 'maxrows 2' ],
+    key = [ 'at graph 1., 1.2', 'maxrows 2', 'width -1.05' ],
     ylabel = 'binding energy (kJ/mol)',
     xlabel = 'metals', rmargin = 0.99, tmargin = 0.85, size='8.5in,8in',
     debug = True

From 6839e81310e1caf58415b767c5b8e1a3505ed795 Mon Sep 17 00:00:00 2001
From: Johanna Huck <jobst@berkeley.edu>
Date: Wed, 24 Jun 2015 13:54:18 -0700
Subject: [PATCH 09/20] fix bw shift, box lt & reverse axis

---
 ccsgp_get_started/dftplots/gp_bindenergy.py | 24 +++++++++++++++------
 1 file changed, 17 insertions(+), 7 deletions(-)

diff --git a/ccsgp_get_started/dftplots/gp_bindenergy.py b/ccsgp_get_started/dftplots/gp_bindenergy.py
index 040d06f..73584be 100644
--- a/ccsgp_get_started/dftplots/gp_bindenergy.py
+++ b/ccsgp_get_started/dftplots/gp_bindenergy.py
@@ -36,21 +36,31 @@ def gp_bindenergy(guest):
     return "guest %s doesn't exist" % guest
   # prepare data
   data = OrderedDict()
-  for file in os.listdir(inDir):
+  files = os.listdir(inDir)
+  nfiles = len(files)
+  dx = 0.7/nfiles
+  gap = (1. - dx*nfiles)/2
+  for idx,file in enumerate(files):
     funct = os.path.splitext(file)[0]
     file_url = os.path.join(inDir, file)
     data[funct] = np.loadtxt(open(file_url, 'rb')) # load data
+    data[funct][:,0] += (idx - nfiles/2 + 0.5*(not nfiles%2)) * dx
   logging.debug(data) # shown if --log flag given on command line
   # generate plot using ccsgp.make_plot
   nSets = len(data)
   make_plot(
     data = data.values(),
-    properties = [ 'with boxes lc %s' % (default_colors[i]) for i in
-                                         range(nSets)],
-    gpcalls = [ 'boxwidth 0.2 absolute', 'style fill solid 1.0 border lt 0',
-               'xtics ("Mg"1, "Mn"2, "Fe"3, "Co"4, "Ni"5, "Cu"6, "Zn"7)'],
-    titles = data.keys(), # use data keys as legend titles
-    name = os.path.join(outDir, guest),
+    properties = [
+        'with boxes lt -1 lc %s' % (default_colors[i]) for i in range(nSets)
+    ], gpcalls = [
+        'boxwidth {} absolute'.format(dx),
+        'style fill solid 1.0 border lt -1',
+        'xtics ("Mg"1, "Mn"2, "Fe"3, "Co"4, "Ni"5, "Cu"6, "Zn"7)',
+        #'object 51 rectangle back fc rgb "grey" from {},0 to {},-60'.format(
+        #    1.5 + gap, 2.5 - gap
+        #),
+    ], titles = data.keys(), # use data keys as legend titles
+    name = os.path.join(outDir, guest), yreverse = True,
     key = [ 'at graph 1., 1.2', 'maxrows 2', 'width -1.05' ],
     ylabel = 'binding energy (kJ/mol)',
     xlabel = 'metals', rmargin = 0.99, tmargin = 0.85, size='8.5in,8in',

From 02b3a300593fcb790a5c3983219b1178a27e70d7 Mon Sep 17 00:00:00 2001
From: Johanna Huck <jobst@berkeley.edu>
Date: Thu, 25 Jun 2015 10:54:33 -0700
Subject: [PATCH 10/20] change x-axis label

---
 ccsgp_get_started/dftplots/gp_bindenergy.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ccsgp_get_started/dftplots/gp_bindenergy.py b/ccsgp_get_started/dftplots/gp_bindenergy.py
index 73584be..a8467f0 100644
--- a/ccsgp_get_started/dftplots/gp_bindenergy.py
+++ b/ccsgp_get_started/dftplots/gp_bindenergy.py
@@ -62,7 +62,7 @@ def gp_bindenergy(guest):
     ], titles = data.keys(), # use data keys as legend titles
     name = os.path.join(outDir, guest), yreverse = True,
     key = [ 'at graph 1., 1.2', 'maxrows 2', 'width -1.05' ],
-    ylabel = 'binding energy (kJ/mol)',
+    ylabel = 'electronic binding energy (kJ/mol)',
     xlabel = 'metals', rmargin = 0.99, tmargin = 0.85, size='8.5in,8in',
     debug = True
   )

From 1f0746e7a7e388729f8b6af2c02be60c06e05147 Mon Sep 17 00:00:00 2001
From: Johanna Huck <jobst@berkeley.edu>
Date: Fri, 26 Jun 2015 16:18:30 -0700
Subject: [PATCH 11/20] add colorscale array for bars

---
 ccsgp_get_started/dftplots/gp_bindenergy.py | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/ccsgp_get_started/dftplots/gp_bindenergy.py b/ccsgp_get_started/dftplots/gp_bindenergy.py
index a8467f0..20f56b3 100644
--- a/ccsgp_get_started/dftplots/gp_bindenergy.py
+++ b/ccsgp_get_started/dftplots/gp_bindenergy.py
@@ -3,7 +3,7 @@
 from collections import OrderedDict
 from ..ccsgp.ccsgp import make_plot
 from ..examples.utils import getWorkDirs
-from ..ccsgp.utils import getOpts
+from ..ccsgp.utils import getOpts, colorscale
 from ..ccsgp.config import default_colors
 
 def gp_bindenergy(guest):
@@ -28,7 +28,16 @@ def gp_bindenergy(guest):
   :ivar funct: functional, filename stem of input file
   :ivar file_url: absolute url to input file
   :ivar nSets: number of datasets
+  :ivar nfiles: number of files
+  :ivar dx: bar width
+  :ivar gap: gap between 2 bars
   """
+  # prepare color arrays for dataset
+  my_color_set = [default_colors[i] for i in range(0, 3)]
+  my_color_array = []
+  for color in my_color_set:
+      my_color_array.append(colorscale(color[-7:-1], 0.8))
+      my_color_array.append(colorscale(color[-7:-1], 1.5))
   # prepare input/output directories
   inDir, outDir = getWorkDirs()
   inDir = os.path.join(inDir, guest)
@@ -42,6 +51,7 @@ def gp_bindenergy(guest):
   gap = (1. - dx*nfiles)/2
   for idx,file in enumerate(files):
     funct = os.path.splitext(file)[0]
+    if funct == 'experiments': continue
     file_url = os.path.join(inDir, file)
     data[funct] = np.loadtxt(open(file_url, 'rb')) # load data
     data[funct][:,0] += (idx - nfiles/2 + 0.5*(not nfiles%2)) * dx
@@ -51,7 +61,7 @@ def gp_bindenergy(guest):
   make_plot(
     data = data.values(),
     properties = [
-        'with boxes lt -1 lc %s' % (default_colors[i]) for i in range(nSets)
+        'with boxes lt -1 lc %s' % (my_color_array[i]) for i in range(nSets)
     ], gpcalls = [
         'boxwidth {} absolute'.format(dx),
         'style fill solid 1.0 border lt -1',

From a537d1b48e817c4e9d7a4925e6a2df0aaa034963 Mon Sep 17 00:00:00 2001
From: Johanna Huck <jobst@berkeley.edu>
Date: Tue, 30 Jun 2015 22:38:30 -0700
Subject: [PATCH 12/20] gp_bindenergy: include experiments

---
 ccsgp_get_started/dftplots/gp_bindenergy.py | 35 +++++++++++----------
 1 file changed, 19 insertions(+), 16 deletions(-)

diff --git a/ccsgp_get_started/dftplots/gp_bindenergy.py b/ccsgp_get_started/dftplots/gp_bindenergy.py
index 20f56b3..2c17051 100644
--- a/ccsgp_get_started/dftplots/gp_bindenergy.py
+++ b/ccsgp_get_started/dftplots/gp_bindenergy.py
@@ -29,15 +29,15 @@ def gp_bindenergy(guest):
   :ivar file_url: absolute url to input file
   :ivar nSets: number of datasets
   :ivar nfiles: number of files
-  :ivar dx: bar width
-  :ivar gap: gap between 2 bars
+  :ivar dx: bar width estimated for specific amount of datasets
+  :ivar gap: space between 2 bars
   """
   # prepare color arrays for dataset
-  my_color_set = [default_colors[i] for i in range(0, 3)]
+  my_color_set = [default_colors[i] for i in range(0, 4)]
   my_color_array = []
   for color in my_color_set:
       my_color_array.append(colorscale(color[-7:-1], 0.8))
-      my_color_array.append(colorscale(color[-7:-1], 1.5))
+      my_color_array.append(colorscale(color[-7:-1], 1.4))
   # prepare input/output directories
   inDir, outDir = getWorkDirs()
   inDir = os.path.join(inDir, guest)
@@ -46,34 +46,37 @@ def gp_bindenergy(guest):
   # prepare data
   data = OrderedDict()
   files = os.listdir(inDir)
-  nfiles = len(files)
+  nfiles = len(files)-1
   dx = 0.7/nfiles
   gap = (1. - dx*nfiles)/2
   for idx,file in enumerate(files):
-    funct = os.path.splitext(file)[0]
-    if funct == 'experiments': continue
+    funct, ext = os.path.splitext(file)
+    if funct == 'experiments' or ext != '.dat': continue
     file_url = os.path.join(inDir, file)
     data[funct] = np.loadtxt(open(file_url, 'rb')) # load data
-    data[funct][:,0] += (idx - nfiles/2 + 0.5*(not nfiles%2)) * dx
+    data[funct][:,0] += (idx - (nfiles+1)/2. + 0.5*(not nfiles%2)) * dx
+  data['M06-L'] = data.pop('M06-L')
+  exp_data = np.loadtxt(open(os.path.join(inDir,'experiments.dat'), 'rb')) # load exp_data
   logging.debug(data) # shown if --log flag given on command line
   # generate plot using ccsgp.make_plot
   nSets = len(data)
   make_plot(
-    data = data.values(),
-    properties = [
+    data = [np.array([[1,-5]])] + data.values(),
+    properties = ['with boxes lt -1 lc %s' % default_colors[-10]] + [
         'with boxes lt -1 lc %s' % (my_color_array[i]) for i in range(nSets)
     ], gpcalls = [
         'boxwidth {} absolute'.format(dx),
         'style fill solid 1.0 border lt -1',
         'xtics ("Mg"1, "Mn"2, "Fe"3, "Co"4, "Ni"5, "Cu"6, "Zn"7)',
-        #'object 51 rectangle back fc rgb "grey" from {},0 to {},-60'.format(
-        #    1.5 + gap, 2.5 - gap
-        #),
-    ], titles = data.keys(), # use data keys as legend titles
+    ] + [
+        'arrow {} from {},{} to {},{} lw 4 lc {} nohead front'.format(
+            i+5, dp[0]-nfiles*dx/2., dp[1], dp[0]+nfiles*dx/2., dp[1], default_colors[-10]
+        ) for i,dp in enumerate(exp_data)
+    ], titles = ['experiments'] + data.keys(), # use data keys as legend titles
     name = os.path.join(outDir, guest), yreverse = True,
-    key = [ 'at graph 1., 1.2', 'maxrows 2', 'width -1.05' ],
+    key = [ 'at graph 1.07, 1.25', 'maxrows 3', 'width -1.1', 'nobox' ],
     ylabel = 'electronic binding energy (kJ/mol)',
-    xlabel = 'metals', rmargin = 0.99, tmargin = 0.85, size='8.5in,8in',
+    xlabel = 'metals', rmargin = 0.99, tmargin = 0.83, size='8.5in,8in',
     debug = True
   )
   return 'done'

From 419bd7fc2ccf5bbff718dc13d98150b52b258b8d Mon Sep 17 00:00:00 2001
From: Johanna Huck <jobst@berkeley.edu>
Date: Wed, 1 Jul 2015 00:14:34 -0700
Subject: [PATCH 13/20] gp_bindenergy: first version of panel plot

---
 ccsgp_get_started/dftplots/gp_bindenergy.py | 90 ++++++++++++---------
 1 file changed, 53 insertions(+), 37 deletions(-)

diff --git a/ccsgp_get_started/dftplots/gp_bindenergy.py b/ccsgp_get_started/dftplots/gp_bindenergy.py
index 2c17051..2545771 100644
--- a/ccsgp_get_started/dftplots/gp_bindenergy.py
+++ b/ccsgp_get_started/dftplots/gp_bindenergy.py
@@ -1,7 +1,7 @@
 import logging, argparse, os, sys
 import numpy as np
 from collections import OrderedDict
-from ..ccsgp.ccsgp import make_plot
+from ..ccsgp.ccsgp import make_panel
 from ..examples.utils import getWorkDirs
 from ..ccsgp.utils import getOpts, colorscale
 from ..ccsgp.config import default_colors
@@ -11,7 +11,7 @@ def gp_bindenergy(guest):
 
   1. prepare input/output directories
   2. load the data into an OrderedDict() [adjust axes units]
-  3. call ccsgp.make_plot with data from 2
+  3. call ccsgp.make_panel with data from 2
 
   Also see::
 
@@ -27,16 +27,16 @@ def gp_bindenergy(guest):
   :ivar file: data input file for specific guest, format: [x y] OR [x y dx dy]
   :ivar funct: functional, filename stem of input file
   :ivar file_url: absolute url to input file
-  :ivar nSets: number of datasets
   :ivar nfiles: number of files
   :ivar dx: bar width estimated for specific amount of datasets
   :ivar gap: space between 2 bars
   """
   # prepare color arrays for dataset
-  my_color_set = [default_colors[i] for i in range(0, 4)]
+  my_color_set = [default_colors[3]] + [default_colors[i] for i in range(0, 3)]
   my_color_array = []
-  for color in my_color_set:
+  for icol,color in enumerate(my_color_set):
       my_color_array.append(colorscale(color[-7:-1], 0.8))
+      if icol == 0: continue
       my_color_array.append(colorscale(color[-7:-1], 1.4))
   # prepare input/output directories
   inDir, outDir = getWorkDirs()
@@ -44,40 +44,56 @@ def gp_bindenergy(guest):
   if not os.path.exists(inDir): # catch missing guest
     return "guest %s doesn't exist" % guest
   # prepare data
-  data = OrderedDict()
-  files = os.listdir(inDir)
-  nfiles = len(files)-1
+  dpt_dict = OrderedDict()
+  dpt_dict['absolute'] = [[], [], []] #dpt
+  # exp-data
+  exp_data = np.loadtxt(open(os.path.join(inDir,'experiments.dat'), 'rb')) # load exp_data
+  dpt_dict['absolute'][0].append(np.array([[1,-5]]))
+  dpt_dict['absolute'][1].append('with boxes lt -1 lc %s' % default_colors[-10])
+  dpt_dict['absolute'][2].append('experiments')
+  # sim-data
+  files = [
+      os.path.join(inDir, funct+ext)
+      for funct,ext in map(os.path.splitext, os.listdir(inDir))
+      if funct != 'experiments' and ext == '.dat'
+  ]
+  nfiles = len(files)
   dx = 0.7/nfiles
   gap = (1. - dx*nfiles)/2
-  for idx,file in enumerate(files):
-    funct, ext = os.path.splitext(file)
-    if funct == 'experiments' or ext != '.dat': continue
-    file_url = os.path.join(inDir, file)
-    data[funct] = np.loadtxt(open(file_url, 'rb')) # load data
-    data[funct][:,0] += (idx - (nfiles+1)/2. + 0.5*(not nfiles%2)) * dx
-  data['M06-L'] = data.pop('M06-L')
-  exp_data = np.loadtxt(open(os.path.join(inDir,'experiments.dat'), 'rb')) # load exp_data
-  logging.debug(data) # shown if --log flag given on command line
-  # generate plot using ccsgp.make_plot
-  nSets = len(data)
-  make_plot(
-    data = [np.array([[1,-5]])] + data.values(),
-    properties = ['with boxes lt -1 lc %s' % default_colors[-10]] + [
-        'with boxes lt -1 lc %s' % (my_color_array[i]) for i in range(nSets)
-    ], gpcalls = [
-        'boxwidth {} absolute'.format(dx),
-        'style fill solid 1.0 border lt -1',
-        'xtics ("Mg"1, "Mn"2, "Fe"3, "Co"4, "Ni"5, "Cu"6, "Zn"7)',
-    ] + [
-        'arrow {} from {},{} to {},{} lw 4 lc {} nohead front'.format(
-            i+5, dp[0]-nfiles*dx/2., dp[1], dp[0]+nfiles*dx/2., dp[1], default_colors[-10]
-        ) for i,dp in enumerate(exp_data)
-    ], titles = ['experiments'] + data.keys(), # use data keys as legend titles
-    name = os.path.join(outDir, guest), yreverse = True,
-    key = [ 'at graph 1.07, 1.25', 'maxrows 3', 'width -1.1', 'nobox' ],
-    ylabel = 'electronic binding energy (kJ/mol)',
-    xlabel = 'metals', rmargin = 0.99, tmargin = 0.83, size='8.5in,8in',
-    debug = True
+  for idx,file_url in enumerate(files):
+      funct = os.path.splitext(os.path.basename(file_url))[0]
+      data_import = np.loadtxt(open(file_url, 'rb')) # load data
+      data_import[:,0] += (idx - nfiles/2. + 0.5*(not nfiles%2)) * dx
+      dpt_dict['absolute'][0].append(data_import)
+      dpt_dict['absolute'][1].append('with boxes lt -1 lc %s' % my_color_array[idx])
+      dpt_dict['absolute'][2].append(funct)
+  # relative differences
+  dpt_dict['relative difference'] = [[], [], []] #dpt
+  for idx,d in enumerate(dpt_dict['absolute'][0][1:]):
+      diff = np.copy(d)
+      exp_data_mod = exp_data if idx != 0 else exp_data[(0,6),:]
+      diff[:,1] /= -exp_data_mod[:,1]
+      diff[:,1] += 1.
+      dpt_dict['relative difference'][0].append(diff)
+      dpt_dict['relative difference'][1].append('with boxes lt -1 lc %s' % my_color_array[idx])
+      dpt_dict['relative difference'][2].append(dpt_dict['absolute'][2][idx+1])
+  logging.debug(dpt_dict) # shown if --log flag given on command line
+  # generate plot using ccsgp.make_panel
+  make_panel(
+      dpt_dict = dpt_dict,
+      gpcalls = [
+          'boxwidth {} absolute'.format(dx),
+          'style fill solid 1.0 border lt -1',
+          'xtics ("Mg"1, "Mn"2, "Fe"3, "Co"4, "Ni"5, "Cu"6, "Zn"7)',
+      ] + [
+          'arrow {} from {},{} to {},{} lw 4 lc {} nohead front'.format(
+              i+5, dp[0]-nfiles*dx/2., dp[1], dp[0]+nfiles*dx/2., dp[1], default_colors[-10]
+          ) for i,dp in enumerate(exp_data)
+      ], name = os.path.join(outDir, guest), yreverse = True,
+      key = [ 'at graph 1.02, 1.17', 'maxrows 2', 'width -1.1', 'nobox' ],
+      ylabel = 'electronic binding energy (kJ/mol)',
+      xlabel = 'metals', rmargin = 0.99, tmargin = 0.88, size='7in,5.5in',
+      debug = True, layout = '1x2'
   )
   return 'done'
 

From dc8e2a4b8fe428a551ec3f1434cd7c7ab7974031 Mon Sep 17 00:00:00 2001
From: Johanna Huck <jobst@berkeley.edu>
Date: Sat, 11 Jul 2015 16:01:49 -0700
Subject: [PATCH 14/20] plots panel-figure for decomposed interaction energies

---
 ccsgp_get_started/dftplots/gp_interaction.py | 90 ++++++++++++++++++++
 1 file changed, 90 insertions(+)
 create mode 100644 ccsgp_get_started/dftplots/gp_interaction.py

diff --git a/ccsgp_get_started/dftplots/gp_interaction.py b/ccsgp_get_started/dftplots/gp_interaction.py
new file mode 100644
index 0000000..e9232e5
--- /dev/null
+++ b/ccsgp_get_started/dftplots/gp_interaction.py
@@ -0,0 +1,90 @@
+import logging, argparse, os, sys
+import numpy as np
+from collections import OrderedDict
+from ..ccsgp.ccsgp import make_panel
+from ..examples.utils import getWorkDirs
+from ..ccsgp.utils import getOpts, colorscale
+from ..ccsgp.config import default_colors
+from string import ascii_lowercase
+
+def gp_interaction():
+  """example for plotting from a text file via numpy.loadtxt
+
+  1. prepare input/output directories
+  2. load the data into an OrderedDict() [adjust axes units]
+  3. call ccsgp.make_panel with data from 2
+
+  Below is an output image for country initial T and the 4 most populated
+  countries for this initial (click to enlarge). Also see::
+
+    $ python -m ccsgp_get_started.examples.gp_datdir -h
+
+  for help on the command line options.
+
+  .. image:: pics/T.png
+     :width: 450 px
+
+  .. image:: pics/U.png
+     :width: 450 px
+
+  :param initial: country initial
+  :type initial: str
+  :param topN: number of most populated countries to plot
+  :type topN: int
+  :ivar inDir: input directory according to package structure and initial
+  :ivar outDir: output directory according to package structure
+  :ivar data: OrderedDict with datasets to plot as separate keys
+  :ivar file: data input file for specific country, format: [x y] OR [x y dx dy]
+  :ivar country: country, filename stem of input file
+  :ivar file_url: absolute url to input file
+  :ivar nSets: number of datasets
+  """
+  # prepare color arrays for dataset
+  my_color_set = [default_colors[i] for i in [0,2]]
+  my_color_array = []
+  for icol, color in enumerate(my_color_set):
+      my_color_array.append(colorscale(color[-7:-1], 0.8))
+      my_color_array.append(colorscale(color[-7:-1], 1.4))
+  # prepare input/output directories
+  inDir, outDir = getWorkDirs()
+  dpt_dict = OrderedDict()
+  for fold_idx,fold in enumerate(['totalE', 'Ex', 'Ec_LDA', 'Ec_vdW']):
+    energy = os.path.splitext(fold)[0]
+    key = '('+list(ascii_lowercase)[fold_idx]+')'
+    # prepare data
+    dpt_dict[key] = [[], [], []] #dpt
+    for index,funct in enumerate(os.listdir(os.path.join(inDir, energy))):
+      funct_name = os.path.splitext(funct)[0]
+      file_url = os.path.join(inDir, energy, funct)
+      data_import = np.loadtxt(open(file_url, 'rb')) #load data
+      data_import[:,0] *= 10.
+      dpt_dict[key][0].append(data_import)
+      dpt_dict[key][1].append('with linespoints lw 4 pt 18 ps 1.5 lt 2 lc %s' %
+                  my_color_array[index])
+      dpt_dict[key][2].append(funct_name)
+  #print dpt_dict
+  logging.debug(dpt_dict) # shown if --log flag given on command line
+  # generate plot using ccsgp.make_plot
+  make_panel(
+    dpt_dict = dpt_dict,
+    name = os.path.join(outDir, 'interaction'),
+    xr = [18, 45.3], yr = [-55, 20],
+    key = ['bottom right', 'maxrows 2', 'width -1.1', 'nobox' ],
+    ylabel = 'DFT binding energy (kJ/mol)',
+    xlabel = 'Mg-O distance, r (nm)', rmargin = 0.98, size='7in,7.5in',
+    lines = {'x=0': 'lc {} lw 4 lt 1'.format(default_colors[-10])},
+    debug = False, layout = '2x2', key_subplot_id = 2
+  )
+  return 'done'
+
+if __name__ == '__main__':
+  parser = argparse.ArgumentParser()
+  #parser.add_argument("initial", help="country initial = input subdir with txt files")
+  #parser.add_argument("topN", help="number of most populated countries to plot")
+  parser.add_argument("--log", help="show log output", action="store_true")
+  args = parser.parse_args()
+  loglevel = 'DEBUG' if args.log else 'WARNING'
+  logging.basicConfig(
+    format='%(message)s', level=getattr(logging, loglevel)
+  )
+  print gp_interaction()

From 34aa975ad6aec002d1cda9cc1de9e732a77a35a8 Mon Sep 17 00:00:00 2001
From: Johanna Huck <jobst@berkeley.edu>
Date: Tue, 11 Aug 2015 11:17:52 +0200
Subject: [PATCH 15/20] add .DS_Store to gitignore

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 2b31cd7..ee4bacc 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,7 @@
 env/*
 *.pyc
 *.swp
+.DS_Store
 output/*
 ccsgp_get_started/.changes
 ccsgp_get_started.egg-info

From 45558f8e4eefec85d4afbd6e7d3cfb9db385753a Mon Sep 17 00:00:00 2001
From: Johanna Huck <jobst@berkeley.edu>
Date: Tue, 11 Aug 2015 11:36:59 +0200
Subject: [PATCH 16/20] update make_panel for metal-guest distance plots

---
 ccsgp_get_started/dftplots/gp_bindenergy.py | 22 +++++++++++++--------
 1 file changed, 14 insertions(+), 8 deletions(-)

diff --git a/ccsgp_get_started/dftplots/gp_bindenergy.py b/ccsgp_get_started/dftplots/gp_bindenergy.py
index 2545771..c83f603 100644
--- a/ccsgp_get_started/dftplots/gp_bindenergy.py
+++ b/ccsgp_get_started/dftplots/gp_bindenergy.py
@@ -79,21 +79,27 @@ def gp_bindenergy(guest):
       dpt_dict['relative difference'][2].append(dpt_dict['absolute'][2][idx+1])
   logging.debug(dpt_dict) # shown if --log flag given on command line
   # generate plot using ccsgp.make_panel
+  exp_data_gpcalls = [
+    'arrow {} from {},{} to {},{} lw 4 lc {} nohead front'.format(
+      i+5, dp[0]-nfiles*dx/2., dp[1], dp[0]+nfiles*dx/2., dp[1], default_colors[-10]
+    ) for i,dp in enumerate(exp_data)
+  ] if use_exp_data else []
+  guest_split = guest.split('_')
+  ylabel = '{} distance for {} binding (nm)'.format(guest_split[0], guest_split[1]) if isM \
+    else 'electronic binding energy (kJ/mol)'
   make_panel(
       dpt_dict = dpt_dict,
       gpcalls = [
           'boxwidth {} absolute'.format(dx),
           'style fill solid 1.0 border lt -1',
           'xtics ("Mg"1, "Mn"2, "Fe"3, "Co"4, "Ni"5, "Cu"6, "Zn"7)',
-      ] + [
-          'arrow {} from {},{} to {},{} lw 4 lc {} nohead front'.format(
-              i+5, dp[0]-nfiles*dx/2., dp[1], dp[0]+nfiles*dx/2., dp[1], default_colors[-10]
-          ) for i,dp in enumerate(exp_data)
-      ], name = os.path.join(outDir, guest), yreverse = True,
+      ] + exp_data_gpcalls,
+      name = os.path.join(outDir, guest), yreverse = (not isM),
       key = [ 'at graph 1.02, 1.17', 'maxrows 2', 'width -1.1', 'nobox' ],
-      ylabel = 'electronic binding energy (kJ/mol)',
-      xlabel = 'metals', rmargin = 0.99, tmargin = 0.88, size='7in,5.5in',
-      debug = True, layout = '1x2'
+      ylabel = ylabel, xlabel = 'metals', rmargin = 0.99,
+      tmargin = 0.93 if guest != 'M-O_H2O_relax' and use_exp_data else 0.88,
+      size='7in,5.5in' if guest != 'M-O_H2O_relax' and use_exp_data else '4in,5.5in',
+      debug = True, layout = '1x2' if guest != 'M-O_H2O_relax' and use_exp_data else '1x1'
   )
   return 'done'
 

From 38fd91de3694960a6a117ded1e336c81f6250f01 Mon Sep 17 00:00:00 2001
From: Johanna Huck <jobst@berkeley.edu>
Date: Tue, 11 Aug 2015 11:42:10 +0200
Subject: [PATCH 17/20] change titles with key entry

---
 ccsgp_get_started/dftplots/gp_bindenergy.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/ccsgp_get_started/dftplots/gp_bindenergy.py b/ccsgp_get_started/dftplots/gp_bindenergy.py
index c83f603..4760f68 100644
--- a/ccsgp_get_started/dftplots/gp_bindenergy.py
+++ b/ccsgp_get_started/dftplots/gp_bindenergy.py
@@ -29,7 +29,6 @@ def gp_bindenergy(guest):
   :ivar file_url: absolute url to input file
   :ivar nfiles: number of files
   :ivar dx: bar width estimated for specific amount of datasets
-  :ivar gap: space between 2 bars
   """
   # prepare color arrays for dataset
   my_color_set = [default_colors[3]] + [default_colors[i] for i in range(0, 3)]
@@ -45,7 +44,10 @@ def gp_bindenergy(guest):
     return "guest %s doesn't exist" % guest
   # prepare data
   dpt_dict = OrderedDict()
-  dpt_dict['absolute'] = [[], [], []] #dpt
+  if 'CO2' in guest: key = '(a)'
+  elif 'CH4' in guest: key = '(b)'
+  else: key = '(a)'
+  dpt_dict[key] = [[], [], []] #dpt
   # exp-data
   exp_data = np.loadtxt(open(os.path.join(inDir,'experiments.dat'), 'rb')) # load exp_data
   dpt_dict['absolute'][0].append(np.array([[1,-5]]))

From 0074d728057d85c2f77565876616312703045814 Mon Sep 17 00:00:00 2001
From: Johanna Huck <jobst@berkeley.edu>
Date: Tue, 11 Aug 2015 11:46:39 +0200
Subject: [PATCH 18/20] prepare input data for metal-guest distance plots

---
 ccsgp_get_started/dftplots/gp_bindenergy.py | 57 ++++++++++++++-------
 1 file changed, 39 insertions(+), 18 deletions(-)

diff --git a/ccsgp_get_started/dftplots/gp_bindenergy.py b/ccsgp_get_started/dftplots/gp_bindenergy.py
index 4760f68..15f5668 100644
--- a/ccsgp_get_started/dftplots/gp_bindenergy.py
+++ b/ccsgp_get_started/dftplots/gp_bindenergy.py
@@ -49,10 +49,22 @@ def gp_bindenergy(guest):
   else: key = '(a)'
   dpt_dict[key] = [[], [], []] #dpt
   # exp-data
-  exp_data = np.loadtxt(open(os.path.join(inDir,'experiments.dat'), 'rb')) # load exp_data
-  dpt_dict['absolute'][0].append(np.array([[1,-5]]))
-  dpt_dict['absolute'][1].append('with boxes lt -1 lc %s' % default_colors[-10])
-  dpt_dict['absolute'][2].append('experiments')
+  exp_filename = os.path.join(inDir,'experiments.dat')
+  use_exp_data = os.path.exists(exp_filename)
+  isM = guest.startswith('M-')
+  if use_exp_data:
+    exp_data = np.loadtxt(open(exp_filename, 'rb')) # load exp_data
+    if len(exp_data.shape) < 2:
+        exp_data = np.array([exp_data])
+    if isM: exp_data[:,1] *= 10.
+  yfake = -5 if use_exp_data else -40
+  if isM: yfake = 1
+  dpt_dict[key][0].append(np.array([[1,yfake]]))
+  dpt_dict[key][1].append(
+    'with boxes lt -1 lc {}'.format(default_colors[-10]) if use_exp_data else \
+    'with lines lc rgb "white"'
+  )
+  dpt_dict[key][2].append('experiments' if use_exp_data else ' ')
   # sim-data
   files = [
       os.path.join(inDir, funct+ext)
@@ -61,24 +73,33 @@ def gp_bindenergy(guest):
   ]
   nfiles = len(files)
   dx = 0.7/nfiles
-  gap = (1. - dx*nfiles)/2
   for idx,file_url in enumerate(files):
       funct = os.path.splitext(os.path.basename(file_url))[0]
       data_import = np.loadtxt(open(file_url, 'rb')) # load data
-      data_import[:,0] += (idx - nfiles/2. + 0.5*(not nfiles%2)) * dx
-      dpt_dict['absolute'][0].append(data_import)
-      dpt_dict['absolute'][1].append('with boxes lt -1 lc %s' % my_color_array[idx])
-      dpt_dict['absolute'][2].append(funct)
+      data_import[:,0] += (idx - (nfiles-1)/2.) * dx
+      if isM: data_import[:,1] *= 10.
+      dpt_dict[key][0].append(data_import)
+      dpt_dict[key][1].append('with boxes lt -1 lc %s' % my_color_array[idx])
+      dpt_dict[key][2].append(funct)
   # relative differences
-  dpt_dict['relative difference'] = [[], [], []] #dpt
-  for idx,d in enumerate(dpt_dict['absolute'][0][1:]):
-      diff = np.copy(d)
-      exp_data_mod = exp_data if idx != 0 else exp_data[(0,6),:]
-      diff[:,1] /= -exp_data_mod[:,1]
-      diff[:,1] += 1.
-      dpt_dict['relative difference'][0].append(diff)
-      dpt_dict['relative difference'][1].append('with boxes lt -1 lc %s' % my_color_array[idx])
-      dpt_dict['relative difference'][2].append(dpt_dict['absolute'][2][idx+1])
+  if guest != 'M-O_H2O_relax' and use_exp_data:
+    dpt_dict[' '] = [[], [], []] #dpt
+    for idx,d in enumerate(dpt_dict[key][0][1:]):
+        if not isM and idx == 4: continue
+        try:
+          exp_data_mod = exp_data if idx != 0 else exp_data[(0,6),:]
+        except:
+          exp_data_mod = np.array([exp_data[0,:]])
+        diff = np.copy(d)
+        if len(diff) != len(exp_data_mod):
+          for i,dp in enumerate(diff):
+            if i >= len(exp_data_mod) or round(dp[0]) != exp_data_mod[i,0]:
+              exp_data_mod = np.insert(exp_data_mod, i, [round(dp[0]), dp[1]], 0)
+        diff[:,1] /= exp_data_mod[:,1]
+        diff[:,1] -= 1.
+        dpt_dict[' '][0].append(diff)
+        dpt_dict[' '][1].append('with boxes lt -1 lc %s' % my_color_array[idx])
+        dpt_dict[' '][2].append(dpt_dict[key][2][idx+1])
   logging.debug(dpt_dict) # shown if --log flag given on command line
   # generate plot using ccsgp.make_panel
   exp_data_gpcalls = [

From e85b2f9ce627be6f23198300502f3c08b54063f6 Mon Sep 17 00:00:00 2001
From: Johanna Huck <jobst@berkeley.edu>
Date: Tue, 11 Aug 2015 13:42:29 +0200
Subject: [PATCH 19/20] fix units for nanometers

---
 ccsgp_get_started/dftplots/gp_bindenergy.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ccsgp_get_started/dftplots/gp_bindenergy.py b/ccsgp_get_started/dftplots/gp_bindenergy.py
index 15f5668..f1f6179 100644
--- a/ccsgp_get_started/dftplots/gp_bindenergy.py
+++ b/ccsgp_get_started/dftplots/gp_bindenergy.py
@@ -56,7 +56,7 @@ def gp_bindenergy(guest):
     exp_data = np.loadtxt(open(exp_filename, 'rb')) # load exp_data
     if len(exp_data.shape) < 2:
         exp_data = np.array([exp_data])
-    if isM: exp_data[:,1] *= 10.
+    if isM: exp_data[:,1] /= 10.
   yfake = -5 if use_exp_data else -40
   if isM: yfake = 1
   dpt_dict[key][0].append(np.array([[1,yfake]]))
@@ -77,7 +77,7 @@ def gp_bindenergy(guest):
       funct = os.path.splitext(os.path.basename(file_url))[0]
       data_import = np.loadtxt(open(file_url, 'rb')) # load data
       data_import[:,0] += (idx - (nfiles-1)/2.) * dx
-      if isM: data_import[:,1] *= 10.
+      if isM: data_import[:,1] /= 10.
       dpt_dict[key][0].append(data_import)
       dpt_dict[key][1].append('with boxes lt -1 lc %s' % my_color_array[idx])
       dpt_dict[key][2].append(funct)

From 95cac1b22686c11958ca23afc4fe5fcb49ed66a2 Mon Sep 17 00:00:00 2001
From: Johanna Huck <jobst@berkeley.edu>
Date: Tue, 11 Aug 2015 13:49:15 +0200
Subject: [PATCH 20/20] same unit fix as in gp_bindenergy

---
 ccsgp_get_started/dftplots/gp_interaction.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ccsgp_get_started/dftplots/gp_interaction.py b/ccsgp_get_started/dftplots/gp_interaction.py
index e9232e5..5755dfa 100644
--- a/ccsgp_get_started/dftplots/gp_interaction.py
+++ b/ccsgp_get_started/dftplots/gp_interaction.py
@@ -57,7 +57,7 @@ def gp_interaction():
       funct_name = os.path.splitext(funct)[0]
       file_url = os.path.join(inDir, energy, funct)
       data_import = np.loadtxt(open(file_url, 'rb')) #load data
-      data_import[:,0] *= 10.
+      data_import[:,0] /= 10.
       dpt_dict[key][0].append(data_import)
       dpt_dict[key][1].append('with linespoints lw 4 pt 18 ps 1.5 lt 2 lc %s' %
                   my_color_array[index])
@@ -68,7 +68,7 @@ def gp_interaction():
   make_panel(
     dpt_dict = dpt_dict,
     name = os.path.join(outDir, 'interaction'),
-    xr = [18, 45.3], yr = [-55, 20],
+    xr = [1.8, 4.53], yr = [-55, 20],
     key = ['bottom right', 'maxrows 2', 'width -1.1', 'nobox' ],
     ylabel = 'DFT binding energy (kJ/mol)',
     xlabel = 'Mg-O distance, r (nm)', rmargin = 0.98, size='7in,7.5in',