refactor the code

.gitignore

@@ -14,3 +14,9 @@
 *.pyc
 CMakeCache.txt
 CMakeFiles
+*.bk
+build
+_skbuild
+deepmd.egg-info
+dist
+

data/raw/raw_to_set.sh

@@ -16,6 +16,7 @@ test -f energy.raw && split energy.raw -l $nline_per_set -d -a 3 energy.raw
 test -f force.raw  && split force.raw  -l $nline_per_set -d -a 3 force.raw
 test -f virial.raw && split virial.raw -l $nline_per_set -d -a 3 virial.raw
 test -f atom_ener.raw && split atom_ener.raw -l $nline_per_set -d -a 3 atom_ener.raw
+test -f fparam.raw && split fparam.raw -l $nline_per_set -d -a 3 fparam.raw
 
 nset=`ls | grep box.raw[0-9] | wc -l`
 nset_1=$(($nset-1))
@@ -32,6 +33,7 @@ do
   test -f force.raw$pi  && mv force.raw$pi  set.$pi/force.raw
   test -f virial.raw$pi && mv virial.raw$pi set.$pi/virial.raw
   test -f atom_ener.raw$pi && mv atom_ener.raw$pi set.$pi/atom_ener.raw
+  test -f fparam.raw$pi && mv fparam.raw$pi set.$pi/fparam.raw
 
   cd set.$pi
   python -c 'import numpy as np; data = np.loadtxt("box.raw"   ); data = data.astype (np.float32); np.save ("box",    data)'
@@ -63,6 +65,13 @@ if os.path.isfile("atom_ener.raw"):
    data = np.loadtxt("atom_ener.raw"); 
    data = data.astype (np.float32); 
    np.save ("atom_ener", data)
+'
+  python -c \
+'import numpy as np; import os.path; 
+if os.path.isfile("fparam.raw"): 
+   data = np.loadtxt("fparam.raw"); 
+   data = data.astype (np.float32); 
+   np.save ("fparam", data)
 '
   rm *.raw
   cd ../

doc/install-tf.1.12.md

@@ -1,18 +1,3 @@
-# Install tensorflow's Python interface 
-We follow the virtual environment approach to install the tensorflow's Python interface. The full instruction can be found on [the tensorflow's official website](https://www.tensorflow.org/install/pip). Now we assume that the Python interface will be installed to virtual environment directory `$tensorflow_venv`
-```bash
-virtualenv --system-site-packages -p python3 $tensorflow_venv
-source $tensorflow_venv/bin/activate
-pip install --upgrade pip
-pip install --upgrade tensorflow==1.12.0
-```
-To verify the installation, 
-```bash
-python -c "import tensorflow as tf; tf.enable_eager_execution(); print(tf.reduce_sum(tf.random_normal([1000, 1000])))"
-```
-
-One should remember to activate the virtual environment every time he/she runs deepmd training program `dp_train`.
-
 # Install tensorflow's C++ interface 
 The tensorflow's C++ interface will be compiled from the source code. Firstly one installs bazel. It is highly recommended that the bazel version 0.15.0 is used. A full instruction of bazel installation can be found [here](https://docs.bazel.build/versions/master/install.html).
 ```bash

doc/install-tf.1.8.md

@@ -1,18 +1,3 @@
-# Install tensorflow's Python interface 
-We follow the virtual environment approach to install the tensorflow's Python interface. The full instruction can be found on [the tensorflow's official website](https://www.tensorflow.org/install/pip). Now we assume that the Python interface will be installed to virtual environment directory `$tensorflow_venv`
-```bash
-virtualenv --system-site-packages -p python3 $tensorflow_venv
-source $tensorflow_venv/bin/activate
-pip install --upgrade pip
-pip install --upgrade tensorflow==1.8.0
-```
-To verify the installation, 
-```bash
-python -c "import tensorflow as tf; sess=tf.Session(); print(sess.run(tf.reduce_sum(tf.random_normal([1000, 1000]))))"
-```
-
-One should remember to activate the virtual environment every time he/she runs deepmd training program `dp_train`.
-
 # Install tensorflow's C++ interface
 The tensorflow's C++ interface will be compiled from the source code. Firstly one installs bazel. It is highly recommended that the bazel version 0.10.0 is used. A full instruction of bazel installation can be found [here](https://docs.bazel.build/versions/master/install.html).
 ```bash

examples/fparam/data/.gitignore

@@ -0,0 +1,2 @@
+*raw
+

examples/fparam/data/e3000_i2000/type.raw

@@ -0,0 +1,54 @@
+0
+0
+0
+0
+0
+0
+0
+0
+0
+0
+0
+0
+0
+0
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+0
+0
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+0
+0
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+0
+0
+0
+0
+0

examples/fparam/data/e8000_i2000/type.raw

@@ -0,0 +1,54 @@
+0
+0
+0
+0
+0
+0
+0
+0
+0
+0
+0
+0
+0
+0
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+0
+0
+0
+0

examples/fparam/lmp/.gitignore

@@ -0,0 +1,3 @@
+frozen_model.pb
+log.lammps
+*dump*

examples/fparam/lmp/conf.lmp

@@ -0,0 +1,64 @@
+
+54 atoms
+1 atom types
+   0.0000000000   10.4280799300 xlo xhi
+   0.0000000000   10.4280799300 ylo yhi
+   0.0000000000   10.4280799300 zlo zhi
+   0.0000000000    0.0000000000    0.0000000000 xy xz yz
+
+Atoms # atomic
+
+     1      1    0.4643750000    0.3949230000   10.2940500000
+     2      1    3.5348720000    0.2520400000   10.3158220000
+     3      1    7.2324620000    0.1228930000   10.1355050000
+     4      1    9.9507070000    3.2752620000    0.0515780000
+     5      1    3.3706880000    3.3152460000   10.3646920000
+     6      1    6.7449020000    3.3255490000   10.2638940000
+     7      1    0.0488410000    6.7351830000   10.3711260000
+     8      1    3.4651590000    7.0327210000    0.1006810000
+     9      1    6.9307650000    6.6957410000    0.1507120000
+    10      1   10.1233330000    0.1368890000    3.3011780000
+    11      1    3.3081460000    0.0219510000    3.4692380000
+    12      1    7.1162540000   10.0116820000    3.8228820000
+    13      1   10.2833810000    3.3816330000    3.5961620000
+    14      1    3.6750080000    3.1843190000    3.9967240000
+    15      1    6.9892550000    3.2920210000    3.6984440000
+    16      1    0.4982230000    7.2412900000    3.2778060000
+    17      1    3.5704530000    6.5520740000    3.4567950000
+    18      1    6.8032210000    7.0392460000    3.4280710000
+    19      1   10.3091590000    0.0994260000    6.8924220000
+    20      1    3.4370550000   10.3684960000    6.9731360000
+    21      1    7.2526880000    9.9857130000    7.1602920000
+    22      1    9.9882210000    3.8193700000    6.5101540000
+    23      1    3.3795490000    3.8468420000    6.9077400000
+    24      1    6.6164890000    3.2631720000    6.7142520000
+    25      1   10.1576680000    7.1165020000    7.2578040000
+    26      1    3.3743670000    6.9032890000    6.7801200000
+    27      1    7.1298310000    6.9588770000    7.2617850000
+    28      1    1.5422020000    2.1329710000    1.5503380000
+    29      1    5.6699180000    1.1054690000    1.7107510000
+    30      1    8.5130900000    1.7898790000    1.6984680000
+    31      1    1.9555310000    5.0886780000    1.5922740000
+    32      1    5.4747010000    4.8624430000    1.7339950000
+    33      1    8.9310980000    5.1557250000    1.8983040000
+    34      1    2.0521660000    8.8521970000    1.9591310000
+    35      1    5.0983580000    8.5203820000    1.4825890000
+    36      1    8.8847120000    8.4793550000    1.6471070000
+    37      1    1.8016150000    1.6971370000    5.4598140000
+    38      1    5.5814970000    1.4779090000    4.8725800000
+    39      1    8.7363780000    1.5159260000    5.4921280000
+    40      1    1.3323340000    5.5041190000    5.5846390000
+    41      1    5.4108570000    5.1845870000    5.4133500000
+    42      1    8.3963130000    5.5316890000    5.1707350000
+    43      1    1.6428930000    9.0357440000    5.3812830000
+    44      1    5.1413850000    8.5704560000    5.1667500000
+    45      1    8.9848480000    8.1466110000    5.0493800000
+    46      1    1.3577270000    2.2488970000    8.1097190000
+    47      1    4.9511170000    1.9240540000    8.3422290000
+    48      1    8.5515580000    2.2705350000    8.3764730000
+    49      1    1.7533270000    5.3976920000    8.8873150000
+    50      1    5.0125090000    5.4878990000    8.8070480000
+    51      1    8.6850970000    4.9585190000    8.8666720000
+    52      1    1.7618510000    8.6701780000    8.7299850000
+    53      1    5.1786470000    8.9149870000    8.5980960000
+    54      1    9.0434810000    9.0196510000    9.0660600000

examples/fparam/lmp/in.lammps

@@ -0,0 +1,25 @@
+# bulk water
+
+units           metal
+boundary        p p p
+atom_style      atomic
+
+neighbor        2.0 bin
+neigh_modify    every 10 delay 0 check no
+
+read_data	conf.lmp
+mass 		1 16
+
+# pair_style	deepmd frozen_model.pb fparam 0.68938740
+pair_style	deepmd frozen_model.pb fparam 0.25852028
+pair_coeff	
+
+velocity        all create 2000 23456789
+
+fix             1 all nvt temp 2000 2000 0.5
+timestep        0.0005
+thermo_style    custom step pe ke etotal temp press vol
+thermo          100
+dump		1 all custom 100 traj.dump id type x y z fx fy fz
+
+run             1000

examples/fparam/train/.gitignore

@@ -0,0 +1,5 @@
+*out
+model.ckpt*
+frozen_model.pb
+checkpoint
+

examples/fparam/train/input.json

@@ -0,0 +1,62 @@
+{
+    "_comment": " model parameters",
+    "model" : {
+	"descriptor": {
+	    "type":		"se_a",
+	    "sel":		[60],
+	    "rcut_smth":	1.80,
+	    "rcut":		6.00,
+	    "neuron":		[25, 50, 100],
+	    "resnet_dt":	false,
+	    "axis_neuron":	8,
+	    "seed":		1
+	},
+	"fitting_net" : {
+	    "neuron":		[120, 120, 120],
+	    "resnet_dt":	true,
+	    "numb_fparam":	1,
+	    "seed":		1
+	}
+    },
+
+    "loss" : {
+	"start_pref_e":	0.02,
+	"limit_pref_e":	1,
+	"start_pref_f":	1000,
+	"limit_pref_f":	1,
+	"start_pref_v":	0,
+	"limit_pref_v":	0
+    },
+
+    "learning_rate" : {
+	"start_lr":	0.001,
+	"decay_steps":	5000,
+	"decay_rate":	0.95
+    },
+
+    "_comment": " traing controls",
+    "training" : {
+	"systems":	["../data/e3000_i2000/", "../data/e8000_i2000/"],
+	"set_prefix":	"set",
+	"stop_batch":	1000000,
+	"batch_size":	1,
+
+	"seed":		1,
+
+	"_comment": " display and restart",
+	"_comment": " frequencies counted in batch",
+	"disp_file":	"lcurve.out",
+	"disp_freq":	100,
+	"numb_test":	10,
+	"save_freq":	1000,
+	"save_ckpt":	"model.ckpt",
+	"load_ckpt":	"model.ckpt",
+	"disp_training":true,
+	"time_training":true,
+	"profiling":	false,
+	"profiling_file":	"timeline.json"
+    },
+
+    "_comment":		"that's all"
+}
+

examples/water/lmp/.gitignore

@@ -0,0 +1,3 @@
+log.lammps
+*.pb
+*.dump

examples/water/train/.gitignore

@@ -0,0 +1,4 @@
+*.out
+*.pb
+model.ckpt*
+checkpoint