upgrade

Change_log.md

@@ -1,16 +1,20 @@
 # [main](https://github.com/jzhang-github/AGAT/tree/main)
-- Fix bugs in high-throughput predict:
-  - [agat/app/cata/generate_adsorption_sites.py](https://github.com/jzhang-github/AGAT/tree/main/agat/app/cata/generate_adsorption_sites.py#L218)
-  - [agat/app/cata/high_throughput_predict.py](https://github.com/jzhang-github/AGAT/tree/main/agat/app/cata/high_throughput_predict.py#L207)
-  - [agat/app/cata/high_throughput_predict.py](https://github.com/jzhang-github/AGAT/tree/main/agat/app/cata/high_throughput_predict.py#L250)
-  - [agat/app/cata/high_throughput_predict.py](https://github.com/jzhang-github/AGAT/tree/main/agat/app/cata/high_throughput_predict.py#L291)
-  - [agat/app/GatApp.py](https://github.com/jzhang-github/AGAT/tree/main/agat/app/GatApp.py#L69-L70)
-  - [agat/default_parameters.py](https://github.com/jzhang-github/AGAT/tree/main/agat/default_parameters.py#L133)
-
-- Deprecate redundant training configurations: train_energy_model, train_force_model, new_energy_train, new_force_train, load_graphs_on_gpu, 
 
-- Modify high-throughput predictions: (These changes are deprecated.)
-	- [agat/app/cata/high_throughput_predict.py#L160](https://github.com/jzhang-github/AGAT/tree/main/agat/app/cata/high_throughput_predict.py#L160), [L169](https://github.com/jzhang-github/AGAT/tree/main/agat/app/cata/high_throughput_predict.py#L169), [L172](https://github.com/jzhang-github/AGAT/tree/main/agat/app/cata/high_throughput_predict.py#L172), [L218](https://github.com/jzhang-github/AGAT/tree/main/agat/app/cata/high_throughput_predict.py#L218), [L245](https://github.com/jzhang-github/AGAT/tree/main/agat/app/cata/high_throughput_predict.py#L245), [L284](https://github.com/jzhang-github/AGAT/tree/main/agat/app/cata/high_throughput_predict.py#L284)
+# [v7.13.2](https://github.com/jzhang-github/AGAT/tree/v7.13.2)
+- Fix bugs in high-throughput predict:
+  - [agat/app/cata/generate_adsorption_sites.py](https://github.com/jzhang-github/AGAT/tree/v7.13.2/agat/app/cata/generate_adsorption_sites.py#L218)
+  - [agat/app/cata/high_throughput_predict.py](https://github.com/jzhang-github/AGAT/tree/v7.13.2/agat/app/cata/high_throughput_predict.py#L207)
+  - [agat/app/cata/high_throughput_predict.py](https://github.com/jzhang-github/AGAT/tree/v7.13.2/agat/app/cata/high_throughput_predict.py#L250)
+  - [agat/app/cata/high_throughput_predict.py](https://github.com/jzhang-github/AGAT/tree/v7.13.2/agat/app/cata/high_throughput_predict.py#L291)
+  - [agat/app/GatApp.py](https://github.com/jzhang-github/AGAT/tree/v7.13.2ain/agat/app/GatApp.py#L69-L70)
+  - [agat/default_parameters.py](https://github.com/jzhang-github/AGAT/tree/v7.13.2/agat/default_parameters.py#L133)
+
+- Deprecate redundant training configurations: 
+	- `train_energy_model`: [agat/model/ModelFit.py](https://github.com/jzhang-github/AGAT/tree/v7.13.2/agat/model/ModelFit.py#L96)  and [agat/model/ModelFit.py](https://github.com/jzhang-github/AGAT/tree/v7.13.2/agat/model/ModelFit.py#L198)
+	- `train_force_model`: [agat/model/ModelFit.py](https://github.com/jzhang-github/AGAT/tree/v7.13.2/agat/model/ModelFit.py#L274) and [agat/model/ModelFit.py](https://github.com/jzhang-github/AGAT/tree/v7.13.2/agat/model/ModelFit.py#L398)
+	- `new_energy_train`
+	- `new_force_train`
+	- `load_graphs_on_gpu`
 
 # [v7.13.1](https://github.com/jzhang-github/AGAT/tree/v7.13.1)
 - Fix a bug here: [agat/model/ModelFit.py](https://github.com/jzhang-github/AGAT/tree/v7.13.1/agat/model/ModelFit.py#L243)

agat/__init__.py

@@ -5,7 +5,7 @@
 @author: ZHANG Jun
 """
 
-__version__ = '7.13。1'
+__version__ = '7.13.2'
 
 import os
 os.environ['DGLBACKEND']="tensorflow"

agat/default_parameters.py

@@ -64,12 +64,8 @@
 
 default_train_config = {
     'dataset_path': 'dataset',
-    'train_energy_model': True,
-    'train_force_model': True,
     'epochs': 1000,
     'output_files': 'out_file',
-    'new_energy_train': False,
-    'new_force_train': False,
     'gpu_for_energy_train': 0,
     'gpu_for_force_train': 0,
     'load_graphs_on_gpu': False, # deprecated

agat/model/ModelFit.py

@@ -93,7 +93,7 @@ def fit_energy_model(self):
                      negative_slope=self.train_config['negative_slope'])
 
         # early stop
-        if self.train_config['early_stop'] and self.train_config['train_energy_model']:
+        if self.train_config['early_stop']: # and self.train_config['train_energy_model']
             stopper = EarlyStopping(energy_model, self.graph_eg, energy_log,
                                     patience=self.train_config['stop_patience'],
                                     folder=os.path.join(self.train_config['output_files'], 'energy_ckpt'))
@@ -195,7 +195,7 @@ def fit_energy_model(self):
                                  PearsonR(en_true_all, en_pred_all), val_mae,
                                  PearsonR(en_val_true, en_val_pred), dur),file=energy_log)
 
-                    if self.train_config['early_stop'] and self.train_config['train_energy_model']:
+                    if self.train_config['early_stop']: # and self.train_config['train_energy_model']
                         if stopper.step(val_mae, energy_model):
                             print('User log: model summary:', file=energy_log)
                             energy_model.summary()
@@ -271,7 +271,7 @@ def fit_force_model(self):
                      tail_readout_no_act=self.train_config['tail_readout_noact'])
 
         # early stop
-        if self.train_config['early_stop'] and self.train_config['train_force_model']:
+        if self.train_config['early_stop']: #  and self.train_config['train_force_model']
             stopper = EarlyStopping(model, self.graph_eg, logf,
                                     patience=self.train_config['stop_patience'],
                                     folder=os.path.join(self.train_config['output_files'], 'force_ckpt'))
@@ -395,7 +395,7 @@ def fit_force_model(self):
                                  force_val_mae, PearsonR(tf.reshape(force_val_true, [-1]), tf.reshape(force_val_pred, [-1])), dur),
                                  file=logf)
 
-                    if self.train_config['early_stop'] and self.train_config['train_force_model']:
+                    if self.train_config['early_stop']: # and self.train_config['train_force_model']
                         if stopper.step(force_val_mae, model):
                             print('User log: model summary:', file=logf)
                             model.summary()

docs/Change_log.html

@@ -39,7 +39,7 @@
   <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="v7.13.1" href="Change_log/Change_log.html" />
+    <link rel="next" title="main" href="Change_log/Change_log.html" />
     <link rel="prev" title="generate_adsorption_sites_ase" href="API_Docs/generate_adsorption_sites_ase.html" /> 
 </head>
 
@@ -105,7 +105,9 @@
 <ul class="current">
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Change log</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="#energy-model">Energy model</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="Change_log/Change_log.html">v7.13.1</a></li>
+<li class="toctree-l3"><a class="reference internal" href="Change_log/Change_log.html">main</a></li>
+<li class="toctree-l3"><a class="reference internal" href="Change_log/Change_log.html#v7-13-2">v7.13.2</a></li>
+<li class="toctree-l3"><a class="reference internal" href="Change_log/Change_log.html#v7-13-1">v7.13.1</a></li>
 <li class="toctree-l3"><a class="reference internal" href="Change_log/Change_log.html#v7-13">v7.13</a></li>
 <li class="toctree-l3"><a class="reference internal" href="Change_log/Change_log.html#v7-12-2">v7.12.2</a></li>
 <li class="toctree-l3"><a class="reference internal" href="Change_log/Change_log.html#v7-12-1">v7.12.1</a></li>
@@ -189,7 +191,9 @@ <h1>Change log<a class="headerlink" href="#change-log" title="Permalink to this
 <h2>Energy model<a class="headerlink" href="#energy-model" title="Permalink to this heading">¶</a></h2>
 <div class="toctree-wrapper compound">
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="Change_log/Change_log.html">v7.13.1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Change_log/Change_log.html">main</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Change_log/Change_log.html#v7-13-2">v7.13.2</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Change_log/Change_log.html#v7-13-1">v7.13.1</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Change_log/Change_log.html#v7-13">v7.13</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Change_log/Change_log.html#v7-12-2">v7.12.2</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Change_log/Change_log.html#v7-12-1">v7.12.1</a></li>
@@ -208,7 +212,7 @@ <h2>Energy model<a class="headerlink" href="#energy-model" title="Permalink to t
 
     <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
 
-        <a href="Change_log/Change_log.html" class="btn btn-neutral float-right" title="v7.13.1" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+        <a href="Change_log/Change_log.html" class="btn btn-neutral float-right" title="main" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
 
 
         <a href="API_Docs/generate_adsorption_sites_ase.html" class="btn btn-neutral float-left" title="generate_adsorption_sites_ase" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>

docs/Change_log/Change_log.html

@@ -9,7 +9,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>v7.13.1 &mdash; AGAT 2022.10.04 documentation</title>
+  <title>main &mdash; AGAT 2022.10.04 documentation</title>
 
 
 
@@ -105,7 +105,9 @@
 <ul class="current">
 <li class="toctree-l1 current"><a class="reference internal" href="../Change_log.html">Change log</a><ul class="current">
 <li class="toctree-l2 current"><a class="reference internal" href="../Change_log.html#energy-model">Energy model</a><ul class="current">
-<li class="toctree-l3 current"><a class="current reference internal" href="#">v7.13.1</a></li>
+<li class="toctree-l3 current"><a class="current reference internal" href="#">main</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#v7-13-2">v7.13.2</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#v7-13-1">v7.13.1</a></li>
 <li class="toctree-l3"><a class="reference internal" href="#v7-13">v7.13</a></li>
 <li class="toctree-l3"><a class="reference internal" href="#v7-12-2">v7.12.2</a></li>
 <li class="toctree-l3"><a class="reference internal" href="#v7-12-1">v7.12.1</a></li>
@@ -166,7 +168,7 @@
 
           <li><a href="../Change_log.html">Change log</a> &raquo;</li>
 
-      <li>v7.13.1</li>
+      <li>main</li>
 
 
       <li class="wy-breadcrumbs-aside">
@@ -185,11 +187,38 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
 
-  <section id="v7-13-1">
+  <section id="main">
+<h1><a class="reference external" href="https://github.com/jzhang-github/AGAT/tree/main">main</a><a class="headerlink" href="#main" title="Permalink to this heading">¶</a></h1>
+</section>
+<section id="v7-13-2">
+<h1><a class="reference external" href="https://github.com/jzhang-github/AGAT/tree/v7.13.2">v7.13.2</a><a class="headerlink" href="#v7-13-2" title="Permalink to this heading">¶</a></h1>
+<ul class="simple">
+<li><p>Fix bugs in high-throughput predict:</p>
+<ul>
+<li><p><a class="reference external" href="https://github.com/jzhang-github/AGAT/tree/v7.13.2/agat/app/cata/generate_adsorption_sites.py#L218">agat/app/cata/generate_adsorption_sites.py</a></p></li>
+<li><p><a class="reference external" href="https://github.com/jzhang-github/AGAT/tree/v7.13.2/agat/app/cata/high_throughput_predict.py#L207">agat/app/cata/high_throughput_predict.py</a></p></li>
+<li><p><a class="reference external" href="https://github.com/jzhang-github/AGAT/tree/v7.13.2/agat/app/cata/high_throughput_predict.py#L250">agat/app/cata/high_throughput_predict.py</a></p></li>
+<li><p><a class="reference external" href="https://github.com/jzhang-github/AGAT/tree/v7.13.2/agat/app/cata/high_throughput_predict.py#L291">agat/app/cata/high_throughput_predict.py</a></p></li>
+<li><p><a class="reference external" href="https://github.com/jzhang-github/AGAT/tree/v7.13.2ain/agat/app/GatApp.py#L69-L70">agat/app/GatApp.py</a></p></li>
+<li><p><a class="reference external" href="https://github.com/jzhang-github/AGAT/tree/v7.13.2/agat/default_parameters.py#L133">agat/default_parameters.py</a></p></li>
+</ul>
+</li>
+<li><p>Deprecate redundant training configurations:</p>
+<ul>
+<li><p><code class="docutils literal notranslate"><span class="pre">train_energy_model</span></code>: <a class="reference external" href="https://github.com/jzhang-github/AGAT/tree/v7.13.2/agat/model/ModelFit.py#L96">agat/model/ModelFit.py</a>  and <a class="reference external" href="https://github.com/jzhang-github/AGAT/tree/v7.13.2/agat/model/ModelFit.py#L198">agat/model/ModelFit.py</a></p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">train_force_model</span></code>: <a class="reference external" href="https://github.com/jzhang-github/AGAT/tree/v7.13.2/agat/model/ModelFit.py#L274">agat/model/ModelFit.py</a> and <a class="reference external" href="https://github.com/jzhang-github/AGAT/tree/v7.13.2/agat/model/ModelFit.py#L398">agat/model/ModelFit.py</a></p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">new_energy_train</span></code></p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">new_force_train</span></code></p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">load_graphs_on_gpu</span></code></p></li>
+</ul>
+</li>
+</ul>
+</section>
+<section id="v7-13-1">
 <h1><a class="reference external" href="https://github.com/jzhang-github/AGAT/tree/v7.13.1">v7.13.1</a><a class="headerlink" href="#v7-13-1" title="Permalink to this heading">¶</a></h1>
 <ul class="simple">
 <li><p>Fix a bug here: <a class="reference external" href="https://github.com/jzhang-github/AGAT/tree/v7.13.1/agat/model/ModelFit.py#L243">agat/model/ModelFit.py</a></p></li>
-<li><p>Load well-trained models: <a class="reference external" href="https://github.com/jzhang-github/AGAT/tree/v7.13.1/agat/model/GatEnergyModel.py#L154-L197">agat/model/GatEnergyModel.py</a> and <a class="reference external" href="https://github.com/jzhang-github/AGAT/tree/v7.13.1/agat/model/GatEnergyForce.py#L201-L246">agat/model/GatForceModel.py</a></p></li>
+<li><p>Load well-trained models: <a class="reference external" href="https://github.com/jzhang-github/AGAT/tree/v7.13.1/agat/model/GatEnergyModel.py#L154-L197">agat/model/GatEnergyModel.py</a> and <a class="reference external" href="https://github.com/jzhang-github/AGAT/tree/v7.13.1/agat/model/GatForceModel.py#L201-L246">agat/model/GatForceModel.py</a></p></li>
 <li><p>Test with best model after training. <a class="reference external" href="https://github.com/jzhang-github/AGAT/tree/v7.13.1/agat/model/ModelFit.py#L222">agat/model/ModelFit.py</a> and <a class="reference external" href="https://github.com/jzhang-github/AGAT/tree/v7.13.1/agat/model/ModelFit.py#L422">agat/model/ModelFit.py</a>.</p></li>
 </ul>
 </section>

docs/Default parameters.html

@@ -96,6 +96,9 @@
 <li class="toctree-l2"><a class="reference internal" href="#default-elements"><code class="docutils literal notranslate"><span class="pre">default_elements</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="#default-build-properties"><code class="docutils literal notranslate"><span class="pre">default_build_properties</span> </code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="#default-data-config"><code class="docutils literal notranslate"><span class="pre">default_data_config</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#default-train-config"><code class="docutils literal notranslate"><span class="pre">default_train_config</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="#default-ase-calculator-config"><code class="docutils literal notranslate"><span class="pre">default_ase_calculator_config</span></code>.</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#default-hp-config"><code class="docutils literal notranslate"><span class="pre">default_hp_config</span></code></a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="Contribution.html">Contribution</a></li>
@@ -382,7 +385,69 @@ <h2><code class="docutils literal notranslate"><span class="pre">default_data_co
 <td>Specify device when building graphs. Negative values for cpu; Positive <code>int</code> for GPU.</td>
 </tr>
 </tbody>
-</table><p><strong>Note</strong>: More <code class="docutils literal notranslate"><span class="pre">num_of_cores</span></code> needs more memory. Weird results happen when you don’t have enough memory.</p>
+</table></section>
+<section id="default-train-config">
+<h2><code class="docutils literal notranslate"><span class="pre">default_train_config</span></code><a class="headerlink" href="#default-train-config" title="Permalink to this heading">¶</a></h2>
+</section>
+<section id="default-ase-calculator-config">
+<h2><code class="docutils literal notranslate"><span class="pre">default_ase_calculator_config</span></code>.<a class="headerlink" href="#default-ase-calculator-config" title="Permalink to this heading">¶</a></h2>
+<p>See <a class="reference external" href="https://gitlab.com/ase/ase/-/blob/master/ase/optimize/bfgs.py">bfgs</a> for more details.</p>
+<table border="1" class="docutils">
+<thead>
+<tr>
+<th>Parameter</th>
+<th>Default value</th>
+<th>Alternative(s)</th>
+<th>Explanation</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>fmax</code></td>
+<td>0.1</td>
+<td><code>float</code></td>
+<td>Convergence criterion of atomic forces. Details: <a href="https://wiki.fysik.dtu.dk/ase/ase/optimize.html#local-optimization">ase optimizer</a></td>
+</tr>
+<tr>
+<td><code>steps</code></td>
+<td>200</td>
+<td><code>int</code></td>
+<td>Maximum iteration steps.</td>
+</tr>
+<tr>
+<td><code>maxstep</code></td>
+<td>0.05</td>
+<td><code>float</code></td>
+<td>maximum distance an atom can move per iteration, unit is Å.</td>
+</tr>
+<tr>
+<td><code>restart</code></td>
+<td><code>None</code></td>
+<td><code>str</code></td>
+<td>Pickle file used to store hessian matrix.</td>
+</tr>
+<tr>
+<td><code>restart_steps</code></td>
+<td>0</td>
+<td><code>int</code></td>
+<td>Restart optimization if the optimization cannot converge.</td>
+</tr>
+<tr>
+<td><code>perturb_steps</code></td>
+<td>0</td>
+<td><code>int</code></td>
+<td>Number of perturbated steps. AGAT may have issues in converging BFGS, perturbating atomic positions may help the convergence.</td>
+</tr>
+<tr>
+<td><code>perturb_amplitude</code></td>
+<td>0.05</td>
+<td><code>float</code></td>
+<td>Perturbation amplitudes if <code>erturb_steps</code> larger than <code>1</code>.</td>
+</tr>
+</tbody>
+</table></section>
+<section id="default-hp-config">
+<h2><code class="docutils literal notranslate"><span class="pre">default_hp_config</span></code><a class="headerlink" href="#default-hp-config" title="Permalink to this heading">¶</a></h2>
 </section>
 </section>