From 6e0b821625e81d86c3a7925e1a46c368292a2bed Mon Sep 17 00:00:00 2001
From: Mingjian Wen <wenxx151@gmail.com>
Date: Thu, 13 Feb 2020 21:39:27 -0800
Subject: [PATCH] Fix CalculatorTorchSeparateSpecies zeta is [] bug

---
 .../auto_examples/auto_examples_jupyter.zip   | Bin 21633 -> 21994 bytes
 .../auto_examples/auto_examples_python.zip    | Bin 16692 -> 17077 bytes
 docs/source/auto_examples/example_nn_Si.ipynb |   7 +++++++
 docs/source/auto_examples/example_nn_Si.py    |   9 +++++++++
 .../source/auto_examples/example_nn_Si.py.md5 |   2 +-
 docs/source/auto_examples/example_nn_Si.rst   |  11 ++++++++++-
 .../example_nn_Si_codeobj.pickle              | Bin 2197 -> 2197 bytes
 .../auto_examples/sg_execution_times.rst      |   8 ++++----
 examples/eg_nn_SiC.py                         |   4 ++--
 examples/example_nn_Si.py                     |   9 +++++++++
 kliff/calculators/calculator_torch.py         |   2 +-
 kliff/nn.py                                   |   4 ++--
 kliff/wrapcalculator.py                       |   6 +++---
 13 files changed, 48 insertions(+), 14 deletions(-)

diff --git a/docs/source/auto_examples/auto_examples_jupyter.zip b/docs/source/auto_examples/auto_examples_jupyter.zip
index 3036946830b71ba597f629252a20bee6cc0c349b..09b4750083ddc20c12b502dcac5c4f9b8e4effbc 100644
GIT binary patch
delta 288
zcmZo%$@pqD<AyY2zG-WG19pV!_?IX$Fq9~6E-`kJn|z-uVzQus<m3mU;`M&{<qGAg
z3K@xIsR|`UiJ5t+DGG^s3VwbHY57G8i3-J;dFeT+3dIGf$(gAN!I^pro@ok|`K1sY
zxurQJnFVn9Vuj4Sm^=jqkb)wG;>zNZ)LfuxDGKF@c_j)Z`3j}QsR}8XX=$lNsX&2(
z#G>HD+|-iPqGGUZ2pNcV#X4ZaN)oeEfiB6(&(Bs!1R9e8a))!gLTW`~F3@g08~p-1
l8~v2bGP@X{?J;?qAF_XDoIERd4w~mDyM&mtF@`b#0RZAwWP$(y

delta 72
zcmaF0nz3;u<AyY2p+hTu15}Sa`^>GtzyQL+43qbVif-;T)|A`)f&B^NWaiL0e5i^h
NuMIV4n-R<a1OV4d7|Q?v

diff --git a/docs/source/auto_examples/auto_examples_python.zip b/docs/source/auto_examples/auto_examples_python.zip
index 048d87a1c91a9a4874140462c7ebbadbaf70fec0..17222e5738fe0916968d1e67e3463a3de81442f7 100644
GIT binary patch
delta 355
zcmZ9Iy-ve06ou0Tqz;IYZdc0C1=$NzrXnT=BBVY*<TTfbNo+^9L&#JK#0X0!-hlxL
zm>K#647^5{ZcMlYfy5c_&v(wfFV~~j+tJf%x_9?@c7Ff1yID_yU_E($pWYnwoBd=-
z2q^6^ipC*$#kz$Sp<tH?&M=`c1EwI3folT{tWbG{U~60mgt;Ja%AwQEupyhuiTby1
zL8t-iCk)umI+PxlLCcf_r=eL|giLUb27RSwhDmg2?6=)tWAL+w1I@7#eU?h=5}4-{
z+axCm;1!eJos2_2=MPJKHG;yq+D4S-!WB(Q7Ftqy(W0VdC3whbTIrNZ=Cc|4L$DO{
ZM5*mQsk?qYd-(Ui{&RM;^Kl$_eE}<`d}jav

delta 59
zcmdnm%DAP8al>JCz8x!l12_|9t8yh67;+^xUsP|Fn0(c72AcTfY9|x65C;Yz004+q
B65s#;

diff --git a/docs/source/auto_examples/example_nn_Si.ipynb b/docs/source/auto_examples/example_nn_Si.ipynb
index b569df60..27752f77 100644
--- a/docs/source/auto_examples/example_nn_Si.ipynb
+++ b/docs/source/auto_examples/example_nn_Si.ipynb
@@ -125,6 +125,13 @@
       "source": [
         "model.save(\"./final_model.pkl\")\nloss.save_optimizer_stat(\"./optimizer_stat.pkl\")\n\nmodel.write_kim_model()"
       ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "<div class=\"alert alert-info\"><h4>Note</h4><p>Now we have trained an NN for a single specie Si. If you have multiple species in\n   your system and want to use different parameters for different species,\n   take a look at the SiC_ example.</p></div>\n\n\n"
+      ]
     }
   ],
   "metadata": {
diff --git a/docs/source/auto_examples/example_nn_Si.py b/docs/source/auto_examples/example_nn_Si.py
index 864c8054..d169845e 100644
--- a/docs/source/auto_examples/example_nn_Si.py
+++ b/docs/source/auto_examples/example_nn_Si.py
@@ -141,3 +141,12 @@
 loss.save_optimizer_stat("./optimizer_stat.pkl")
 
 model.write_kim_model()
+
+
+##########################################################################################
+# .. note::
+#    Now we have trained an NN for a single specie Si. If you have multiple species in
+#    your system and want to use different parameters for different species,
+#    take a look at the SiC_ example.
+#
+# .. _SiC: https://github.com/mjwen/kliff/blob/master/examples/eg_nn_SiC.py
diff --git a/docs/source/auto_examples/example_nn_Si.py.md5 b/docs/source/auto_examples/example_nn_Si.py.md5
index 702d4469..9b2a8f25 100644
--- a/docs/source/auto_examples/example_nn_Si.py.md5
+++ b/docs/source/auto_examples/example_nn_Si.py.md5
@@ -1 +1 @@
-99c760f443633dcf0ce755d5995447f7
\ No newline at end of file
+6baccb59d251b6e52d886f0ec66aa7ae
\ No newline at end of file
diff --git a/docs/source/auto_examples/example_nn_Si.rst b/docs/source/auto_examples/example_nn_Si.rst
index 929a71c0..c2871501 100644
--- a/docs/source/auto_examples/example_nn_Si.rst
+++ b/docs/source/auto_examples/example_nn_Si.rst
@@ -242,6 +242,8 @@ codes such as LAMMPS via the KIM API.
 
 
 
+
+
 .. rst-class:: sphx-glr-script-out
 
  Out:
@@ -253,10 +255,17 @@ codes such as LAMMPS via the KIM API.
 
 
 
+.. note::
+   Now we have trained an NN for a single specie Si. If you have multiple species in
+   your system and want to use different parameters for different species,
+   take a look at the SiC_ example.
+
+.. _SiC: https://github.com/mjwen/kliff/blob/master/examples/eg_nn_SiC.py
+
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  16.523 seconds)
+   **Total running time of the script:** ( 0 minutes  16.575 seconds)
 
 
 .. _sphx_glr_download_auto_examples_example_nn_Si.py:
diff --git a/docs/source/auto_examples/example_nn_Si_codeobj.pickle b/docs/source/auto_examples/example_nn_Si_codeobj.pickle
index c31fa6eaf825c85e010df52149cd243b10561b90..a3c6b2c07dde1cf8cf7ed988d057edaa32b81caf 100644
GIT binary patch
delta 209
zcmbO#I8|_h-sA{I8TKBQyu{qpDU-_>l{kCYa`RJ4bAY@Ub~*kY9tbbKI3vHPWXj}S
zjBb->GWk!oXNj52&Z@>JH+d#Y-efuU{K;yJMw7XiT_*RkhfQ{73Y)~_JlTg$lhJkZ
zYc}J_kJ%$8FJSYVT*;=w7%}-WbI#<=%<_zhlb<muGNw*G!s;;bbo69vj)=+ntkWm^
zF{i3=rKA=o7iAWd<QGk;ouZM!)*}#HnVXwhQdH?ynwMOXnV&Z$gJWWX?&PVghLc&?
I+?h)C0L5cRAOHXW

delta 209
zcmbO#I8|_ho)K3{YH@N=W<g1Q(UjUL8a*s|iMgp$dIW+ib8}NmiYnbo^O8$4^Yf<k
zu;u2bl;)&Pnf#7jm%oPx!iz7?$S*1Zi%k}1i=8}=$!MaU3{wW%#6YFV+>FK(cbQH;
z!0bFZi#crKd;iHhS>+jxCZA(+o1Dy^%FN_vG<grJ45PzjZPuL0c8oET4>RUWp2euf
z7(Dqj+l<M#S?wnKaJWxqV$otuo6O9r&X_fM8%w}s0~UkH`b_zgMVP}TC$L0JE@6vc
HD%Ar3j(A8d

diff --git a/docs/source/auto_examples/sg_execution_times.rst b/docs/source/auto_examples/sg_execution_times.rst
index 1c8042bb..4d48b35c 100644
--- a/docs/source/auto_examples/sg_execution_times.rst
+++ b/docs/source/auto_examples/sg_execution_times.rst
@@ -5,12 +5,12 @@
 
 Computation times
 =================
-**01:57.516** total execution time for **auto_examples** files:
+**00:16.575** total execution time for **auto_examples** files:
 
 +-----------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_auto_examples_example_kim_SW_Si.py` (``example_kim_SW_Si.py``)                 | 01:40.195 | 0.0 MB |
+| :ref:`sphx_glr_auto_examples_example_nn_Si.py` (``example_nn_Si.py``)                         | 00:16.575 | 0.0 MB |
 +-----------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_auto_examples_example_nn_Si.py` (``example_nn_Si.py``)                         | 00:16.523 | 0.0 MB |
+| :ref:`sphx_glr_auto_examples_example_kim_SW_Si.py` (``example_kim_SW_Si.py``)                 | 00:00.000 | 0.0 MB |
 +-----------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_auto_examples_example_linear_regression.py` (``example_linear_regression.py``) | 00:00.798 | 0.0 MB |
+| :ref:`sphx_glr_auto_examples_example_linear_regression.py` (``example_linear_regression.py``) | 00:00.000 | 0.0 MB |
 +-----------------------------------------------------------------------------------------------+-----------+--------+
diff --git a/examples/eg_nn_SiC.py b/examples/eg_nn_SiC.py
index 66906cc3..cc6b05c4 100644
--- a/examples/eg_nn_SiC.py
+++ b/examples/eg_nn_SiC.py
@@ -1,10 +1,10 @@
 """
-.. _tut_nn:
+.. _tut_nn_multi_spec:
 
 Train a neural network potential
 ================================
 
-In this tutorial, we train a neural network (NN) potential for silicon
+In this tutorial, we train a neural network (NN) potential for SiC
 """
 
 
diff --git a/examples/example_nn_Si.py b/examples/example_nn_Si.py
index 864c8054..d169845e 100644
--- a/examples/example_nn_Si.py
+++ b/examples/example_nn_Si.py
@@ -141,3 +141,12 @@
 loss.save_optimizer_stat("./optimizer_stat.pkl")
 
 model.write_kim_model()
+
+
+##########################################################################################
+# .. note::
+#    Now we have trained an NN for a single specie Si. If you have multiple species in
+#    your system and want to use different parameters for different species,
+#    take a look at the SiC_ example.
+#
+# .. _SiC: https://github.com/mjwen/kliff/blob/master/examples/eg_nn_SiC.py
diff --git a/kliff/calculators/calculator_torch.py b/kliff/calculators/calculator_torch.py
index 2a198999..1a73d190 100644
--- a/kliff/calculators/calculator_torch.py
+++ b/kliff/calculators/calculator_torch.py
@@ -248,7 +248,7 @@ def compute(self, batch):
         for s, zeta in zeta_by_species.items():
 
             # have no species "s" in this batch of data
-            if zeta is []:
+            if not zeta:  # zeta == []
                 continue
 
             z_tensor = torch.stack(zeta)  # convert a list of tensor to tensor
diff --git a/kliff/nn.py b/kliff/nn.py
index d0b18053..c28c4dfd 100644
--- a/kliff/nn.py
+++ b/kliff/nn.py
@@ -31,12 +31,12 @@ def forward(self, input):
             shape_4D = (1, *shape, 1)
         elif dim == 3:
             if shape[0] != 1:
-                raise Exception('Shape[0] needs to be 1 for a 3D tensor.')
+                raise Exception("Shape[0] needs to be 1 for a 3D tensor.")
             shape_4D = (*shape, 1)
 
         else:
             raise Exception(
-                'Input need to be 2D or 3D tensor, but got a ' '{}D tensor.'.format(dim)
+                "Input need to be 2D or 3D tensor, but got a " "{}D tensor.".format(dim)
             )
         x = torch.reshape(input, shape_4D)
         x = torch.transpose(x, 1, 2)
diff --git a/kliff/wrapcalculator.py b/kliff/wrapcalculator.py
index a67620a4..7c422000 100644
--- a/kliff/wrapcalculator.py
+++ b/kliff/wrapcalculator.py
@@ -41,7 +41,7 @@ def _update_params(self):
         """Write parameters to file KIM_MODEL_PARAMS + modelname, and also give its path to the
         enviroment variable that has the same name: KIM_MODEL_PARAMS + modelname.
         """
-        name = 'KIM_MODEL_PARAMS_' + self.params._modelname
+        name = "KIM_MODEL_PARAMS_" + self.params._modelname
         self.params.echo_params(name, print_size=True)
         path = os.getcwd() + os.path.sep + name
         os.environ[name] = path
@@ -59,13 +59,13 @@ def _parse_edn(self, fname, keys):
           Keyword in the edn format(think it as a dictionary), whose value will be returned.
         """
 
-        with open(fname, 'r') as fin:
+        with open(fname, "r") as fin:
             lines = fin.read()
         parsed = edn_format.loads(lines)
         values = []
         for k in keys:
             try:
-                v = parsed[k]['source-value']
+                v = parsed[k]["source-value"]
             except KeyError:
                 raise KeyError('Keyword "{}" not found in {}.'.format(k, self.outname))
             # make it a 1D array