From 626b6aadc1af0b2b0feba6ce9515ecece0461ae5 Mon Sep 17 00:00:00 2001 From: jyxu Date: Mon, 17 Oct 2022 00:05:11 +0100 Subject: [PATCH] update docs --- docs/build/doctrees/environment.pickle | Bin 427580 -> 430265 bytes docs/build/doctrees/start.doctree | Bin 21991 -> 21997 bytes docs/build/html/_sources/start.rst.txt | 10 ++-------- docs/build/html/searchindex.js | 2 +- docs/build/html/start.html | 4 ++-- .../source/_build/doctrees/environment.pickle | Bin 427002 -> 427002 bytes docs/source/_build/doctrees/start.doctree | Bin 21991 -> 21997 bytes .../source/_build/html/_sources/start.rst.txt | 10 ++-------- docs/source/_build/html/searchindex.js | 2 +- docs/source/_build/html/start.html | 4 ++-- docs/source/start.rst | 10 ++-------- 11 files changed, 12 insertions(+), 30 deletions(-) diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle index 6ab69359dc90159e5a177182cf557423337ce0ec..3ecd3185e421612d62fe52c75bf91bf91a2e05eb 100644 GIT binary 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Units ----- - We use the following units through all input files: Time ``fs``, Length ``AA``, Energy ``eV``, Force ``eV/AA``. Potential --------- - We have supported several MLIP formulations based on an ``AbstractPotentialManager`` class to access **driver**, **expedition**, and **training** through workflows. @@ -35,7 +32,6 @@ See :ref:`Potential Examples` section for more details. Driver ------ - After potential is defined, we need to further specify what simulation would be perfomed in the **driver** section. A driver (``AbstractDriver``) is the basic unit with an attacthed **ase** ``calculators`` for basic dynamics tasks, namely, @@ -61,10 +57,9 @@ See :ref:`Driver Examples` section for more details. Scheduler --------- - With **potential** and **driver** defined, we can run simulations on local machines (directly in the command line). However, simulations, under most -circumstances, would be really heavy even by MLIPs (image a 10 ns molecular +circumstances, would be really heavy even by MLIPs (imagine a 10 ns molecular dynamics). The simulations would ideally be dispatched to high performace clusters (HPCs). @@ -86,7 +81,6 @@ The example below shows how to define a **scheduler** in a **yaml** file: Worker ------ - **Worker** that combines the above components is what we use throughout various workflows to deal with computations. @@ -115,7 +109,7 @@ The example below shows how to define a **worker** in a **yaml** file: time: "0:10:00" environs: "source ~/envs/source_eann.sh\nconda activate catorch2\n" -to run a **nvt** simulation with given structures by **nequip** on a **slurm** +to run a **nvt** simulation with given structures by **deepmd** on a **slurm** machine .. code-block:: shell diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js index d0699bc4..8a8f4b82 100644 --- a/docs/build/html/searchindex.js +++ b/docs/build/html/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["about", "computations/index", "expeditions/ads", "expeditions/evo", "expeditions/index", 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DriverSchedulerΒΆ

With potential and driver defined, we can run simulations on local machines (directly in the command line). However, simulations, under most -circumstances, would be really heavy even by MLIPs (image a 10 ns molecular +circumstances, would be really heavy even by MLIPs (imagine a 10 ns molecular dynamics). The simulations would ideally be dispatched to high performace clusters (HPCs).

The example below shows how to define a scheduler in a yaml file:

@@ -269,7 +269,7 @@

Workerenvirons: "source ~/envs/source_eann.sh\nconda activate catorch2\n" -

to run a nvt simulation with given structures by nequip on a slurm +

to run a nvt simulation with given structures by deepmd on a slurm machine

# -- submit jobs...
 #    one structure for one job
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diff --git a/docs/source/_build/html/_sources/start.rst.txt b/docs/source/_build/html/_sources/start.rst.txt
index 2a28cb3c..427c4333 100644
--- a/docs/source/_build/html/_sources/start.rst.txt
+++ b/docs/source/_build/html/_sources/start.rst.txt
@@ -1,20 +1,17 @@
 Getting Started
 ===============
-
 Here, we would introduce several basic components of GDPy, namely **potential**, 
 **driver**, **worker**. **Worker** is the basic unit that performs any 
 computation, which contains a ``AbstractPotentialManager`` and a ``Scheduler``.
 
 Units
 -----
-
 We use the following units through all input files:
 
 Time ``fs``, Length ``AA``, Energy ``eV``, Force ``eV/AA``.
 
 Potential
 ---------
-
 We have supported several MLIP formulations based on an ``AbstractPotentialManager`` 
 class to access **driver**, **expedition**, and **training** through workflows. 
 
@@ -35,7 +32,6 @@ See :ref:`Potential Examples` section for more details.
 
 Driver
 ------
-
 After potential is defined, we need to further specify what simulation would be 
 perfomed in the **driver** section. A driver (``AbstractDriver``) is the basic 
 unit with an attacthed **ase** ``calculators`` for basic dynamics tasks, namely, 
@@ -61,10 +57,9 @@ See :ref:`Driver Examples` section for more details.
 
 Scheduler
 ---------
-
 With **potential** and **driver** defined, we can run simulations on local 
 machines (directly in the command line). However, simulations, under most 
-circumstances, would be really heavy even by MLIPs (image a 10 ns molecular 
+circumstances, would be really heavy even by MLIPs (imagine a 10 ns molecular 
 dynamics). The simulations would ideally be dispatched to high performace clusters
 (HPCs).
 
@@ -86,7 +81,6 @@ The example below shows how to define a **scheduler** in a **yaml** file:
 
 Worker
 ------
-
 **Worker** that combines the above components is what we use throughout various 
 workflows to deal with computations. 
 
@@ -115,7 +109,7 @@ The example below shows how to define a **worker** in a **yaml** file:
         time: "0:10:00"
         environs: "source ~/envs/source_eann.sh\nconda activate catorch2\n"
 
-to run a **nvt** simulation with given structures by **nequip** on a **slurm** 
+to run a **nvt** simulation with given structures by **deepmd** on a **slurm** 
 machine
 
 .. code-block:: shell
diff --git a/docs/source/_build/html/searchindex.js b/docs/source/_build/html/searchindex.js
index ac7266a2..543dcb21 100644
--- a/docs/source/_build/html/searchindex.js
+++ b/docs/source/_build/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["about", "computations/index", "expeditions/ads", "expeditions/evo", "expeditions/index", "expeditions/md", "expeditions/rxn", "extensions/index", "index", "installation", "modules/builder", "modules/computation", "modules/computation.uncertainty", "modules/computation.worker", "modules/config", "modules/expedition", "modules/main", "modules/modules", "modules/potential", "modules/potential.managers", "modules/reaction", "modules/scheduler", "modules/selector", "modules/trainer", "potentials/index", "start", "tutorials/copper", "tutorials/index", "tutorials/water"], "filenames": ["about.rst", "computations/index.rst", "expeditions/ads.rst", "expeditions/evo.rst", "expeditions/index.rst", "expeditions/md.rst", "expeditions/rxn.rst", "extensions/index.rst", "index.rst", "installation.rst", "modules/builder.rst", "modules/computation.rst", "modules/computation.uncertainty.rst", "modules/computation.worker.rst", "modules/config.rst", "modules/expedition.rst", "modules/main.rst", "modules/modules.rst", "modules/potential.rst", "modules/potential.managers.rst", "modules/reaction.rst", "modules/scheduler.rst", "modules/selector.rst", "modules/trainer.rst", "potentials/index.rst", "start.rst", "tutorials/copper.rst", "tutorials/index.rst", "tutorials/water.rst"], "titles": ["About", "Computations", "Explore Adsorbate Configurations", "Explore with Global Optimisation", "Expeditions", "Explore with Molecular Dynamics (MD)", "Explore Chemical Reactions", "Extensions", "GDPy Documentation", "Installation", "builder package", "computation package", "computation.uncertainty package", "computation.worker package", "config module", "expedition package", "main module", "GDPy", "potential package", "potential.managers package", "reaction package", "scheduler package", "selector package", "trainer package", "Potentials", "Getting Started", "Build a Potential for Cu Bulk with Global Search", "Tutorials", "Build a Potential for Pt/H2O with On-the-Fly 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\ No newline at end of file
diff --git a/docs/source/_build/html/start.html b/docs/source/_build/html/start.html
index f18d1ccb..9dc550a2 100644
--- a/docs/source/_build/html/start.html
+++ b/docs/source/_build/html/start.html
@@ -224,7 +224,7 @@ 
DriverSchedulerΒΆ

 
With potential and driver defined, we can run simulations on local
 machines (directly in the command line). However, simulations, under most
-circumstances, would be really heavy even by MLIPs (image a 10 ns molecular
+circumstances, would be really heavy even by MLIPs (imagine a 10 ns molecular
 dynamics). The simulations would ideally be dispatched to high performace clusters
 (HPCs).

 
The example below shows how to define a scheduler in a yaml file:

@@ -269,7 +269,7 @@ 
Workerenvirons: "source ~/envs/source_eann.sh\nconda activate catorch2\n"
-

to run a nvt simulation with given structures by nequip on a slurm +

to run a nvt simulation with given structures by deepmd on a slurm machine

# -- submit jobs...
 #    one structure for one job
diff --git a/docs/source/start.rst b/docs/source/start.rst
index 2a28cb3c..427c4333 100644
--- a/docs/source/start.rst
+++ b/docs/source/start.rst
@@ -1,20 +1,17 @@
 Getting Started
 ===============
-
 Here, we would introduce several basic components of GDPy, namely **potential**, 
 **driver**, **worker**. **Worker** is the basic unit that performs any 
 computation, which contains a ``AbstractPotentialManager`` and a ``Scheduler``.
 
 Units
 -----
-
 We use the following units through all input files:
 
 Time ``fs``, Length ``AA``, Energy ``eV``, Force ``eV/AA``.
 
 Potential
 ---------
-
 We have supported several MLIP formulations based on an ``AbstractPotentialManager`` 
 class to access **driver**, **expedition**, and **training** through workflows. 
 
@@ -35,7 +32,6 @@ See :ref:`Potential Examples` section for more details.
 
 Driver
 ------
-
 After potential is defined, we need to further specify what simulation would be 
 perfomed in the **driver** section. A driver (``AbstractDriver``) is the basic 
 unit with an attacthed **ase** ``calculators`` for basic dynamics tasks, namely, 
@@ -61,10 +57,9 @@ See :ref:`Driver Examples` section for more details.
 
 Scheduler
 ---------
-
 With **potential** and **driver** defined, we can run simulations on local 
 machines (directly in the command line). However, simulations, under most 
-circumstances, would be really heavy even by MLIPs (image a 10 ns molecular 
+circumstances, would be really heavy even by MLIPs (imagine a 10 ns molecular 
 dynamics). The simulations would ideally be dispatched to high performace clusters
 (HPCs).
 
@@ -86,7 +81,6 @@ The example below shows how to define a **scheduler** in a **yaml** file:
 
 Worker
 ------
-
 **Worker** that combines the above components is what we use throughout various 
 workflows to deal with computations. 
 
@@ -115,7 +109,7 @@ The example below shows how to define a **worker** in a **yaml** file:
         time: "0:10:00"
         environs: "source ~/envs/source_eann.sh\nconda activate catorch2\n"
 
-to run a **nvt** simulation with given structures by **nequip** on a **slurm** 
+to run a **nvt** simulation with given structures by **deepmd** on a **slurm** 
 machine
 
 .. code-block:: shell