docs/examples fix (#140)

* DMC_fix * udpate gitignore and delete .idea cache --------- Co-authored-by: Yingze Wang <[email protected]>
deepmodeling · Nov 8, 2023 · 8ffb4fb · 8ffb4fb
1 parent e0b0f15
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diff --git a/.gitignore b/.gitignore
@@ -789,3 +789,6 @@ FodyWeavers.xsd
 # debugging ipynb
 debug.ipynb
 test.xml
+
+# PyCharm Cache
+.idea/
diff --git a/docs/dev_guide/generator.ipynb b/docs/dev_guide/generator.ipynb
diff --git a/docs/user_guide/1.introduction.md b/docs/user_guide/1.introduction.md
@@ -7,7 +7,6 @@ In this user guide, you will learn:
 - [New modules release](./4.modules.md)
 - [Advanced examples](./DMFF_example.ipynb) of DMFF, which can help you quickly get started with DMFF
 
-
 The first thing you should know is that DMFF is not an actual force field model (such as OPLS or AMBER), but a differentiable implementation of various force field (or "potential") functional forms. It contains following modules:
 
 - Classical module: implements classical force fields (OPLS or GAFF like potentials)

diff --git a/docs/user_guide/4.modules.md b/docs/user_guide/4.modules.md
@@ -2,10 +2,10 @@
 
 In this part, you will see 7 modules of DMFF, some of which are newly released in version 1.0.0. Let's get started with them:
 
-+ [Classical](docs/user_guide/4.1classical.md)
-+ [ADMP](docs/user_guide/4.2ADMPPmeForce.md)
-+ [Qeq](docs/user_guide/4.3ADMPQeqForce.md)
-+ [Machine Learning](docs/user_guide/4.4MLForce.md)
-+ [Optimization](docs/user_guide/4.5Optimization.md)
-+ [Mbar Estimator](docs/user_guide/4.6MBAR.md)
-+ [OpenMM Plugin](docs/user_guide/4.7OpenMMplugin.md)
++ [Classical](./4.1classical.md)
++ [ADMP](./4.2ADMPPmeForce.md)
++ [Qeq](./4.3ADMPQeqForce.md)
++ [Machine Learning](./4.4MLForce.md)
++ [Optimization](./4.5Optimization.md)
++ [Mbar Estimator](./4.6MBAR.md)
++ [OpenMM Plugin](./4.7OpenMMplugin.md)
diff --git a/examples/DMC/init.dcd b/examples/DMC/init.dcd
diff --git a/examples/DMC/lj.xml b/examples/DMC/lj.xml
@@ -0,0 +1,19 @@
+<ForceField>
+<AtomTypes>
+<Type element="C" name="cm" class="cm" mass="15.035"/>
+<Type element="C" name="co" class="co" mass="60.008"/>
+</AtomTypes>
+<Residues>
+<Residue name="DMC">
+<Atom name="CM1" type="cm"/>
+<Atom name="CM2" type="cm"/>
+<Atom name="CO" type="co"/>
+<Bond atomName1="CM1" atomName2="CO"/>
+<Bond atomName1="CM2" atomName2="CO"/>
+</Residue>
+</Residues>
+<LennardJonesForce lj14scale="0.50000">
+<Atom type="cm" sigma="0.50" epsilon="0.75" charge="0.2841"/>
+<Atom type="co" sigma="0.50" epsilon="0.75" charge="-0.5682"/>
+</LennardJonesForce>
+</ForceField>
diff --git a/examples/DMC/res.xml b/examples/DMC/res.xml
@@ -0,0 +1,23 @@
+<ForceField>
+<AtomTypes>
+<Type element="C" name="cm" class="cm" mass="15.035"/>
+<Type element="C" name="co" class="co" mass="60.008"/>
+</AtomTypes>
+<Residues>
+<Residue name="DMC">
+<Atom name="CM1" type="cm"/>
+<Atom name="CM2" type="cm"/>
+<Atom name="CO" type="co"/>
+<Bond atomName1="CM1" atomName2="CO"/>
+<Bond atomName1="CM2" atomName2="CO"/>
+</Residue>
+</Residues>
+<HarmonicBondForce>
+<Bond class1="cm" class2="co" length="0.141000" k="267776.000000"/>
+</HarmonicBondForce>
+<HarmonicAngleForce>
+<Angle class1="cm" class2="co" class3="cm" angle="2.062630" k="584.923200"/>
+</HarmonicAngleForce>
+<NonbondedForce coulomb14scale="0.5" lj14scale="0.5">
+</NonbondedForce>
+</ForceField>
diff --git a/examples/mbar/ben-prm.xml b/examples/mbar/ben-prm.xml
diff --git a/examples/mbar/ben-top.xml b/examples/mbar/ben-top.xml
diff --git a/examples/mbar/ben.pdb b/examples/mbar/ben.pdb
diff --git a/examples/mbar/benz.txt b/examples/mbar/benz.txt