From 05e736aead528db8bb6e9d31645e055074379c2d Mon Sep 17 00:00:00 2001 From: Jiahao Xie <2986086188@qq.com> Date: Fri, 15 May 2026 19:58:28 +0800 Subject: [PATCH 1/4] docs(scan): add SD/CG/SD-CG method pages and sync with debug/OPT - Add tasks/scan/scan_sd.html, scan_cg.html, scan_sdcg.html for relaxed scans with the SD, CG, and SD/CG optimizers; parameters mirror the corresponding #opt(method=...) pages. - Rework tasks/scan/scan.html with an Available Methods table, Quick Usage block, Common Parameters table, and the real example/scan/da.inp two-coordinate example; correct n_steps semantics to "initial point + n_steps". - Update scan_lbfgs.html and scan_rfo.html to reflect the unified optimization dispatcher; drop the warning that RFO scans are unsupported and align defaults with the runtime. - Wire CG and SD/CG into every page sidebar (Optimization + PES Scan trees) and refresh scan-related copy in setup, functions, tutorials, index/general/development/home1, and the IRC entry point. - Note the debug/OPT sync on downloads.html so visitors know the public upstream may lag the documented scan features. --- development.html | 2 +- downloads.html | 3 +- functions/constrain.html | 62 ++++----- functions/solvent.html | 5 + general.html | 2 +- home1.html | 6 +- index.html | 2 +- setup/coordinates.html | 23 ++-- setup/model_aimnet.html | 5 + setup/model_ani.html | 5 + setup/model_mace.html | 5 + setup/model_uma.html | 5 + setup/models.html | 5 + setup/settings.html | 13 +- tasks/frequency.html | 5 + tasks/irc/irc.html | 7 +- tasks/irc/irc_eulerpc.html | 5 + tasks/irc/irc_gs.html | 5 + tasks/irc/irc_hpc.html | 5 + tasks/irc/irc_lqa.html | 5 + tasks/opt/opt_cg.html | 4 + tasks/opt/opt_lbfgs.html | 3 + tasks/opt/opt_rfo.html | 3 + tasks/opt/opt_sd.html | 3 + tasks/opt/opt_sdcg.html | 4 + tasks/opt/optimization.html | 5 +- tasks/scan/scan.html | 232 ++++++++++++++++++++----------- tasks/scan/scan_cg.html | 254 ++++++++++++++++++++++++++++++++++ tasks/scan/scan_lbfgs.html | 70 ++++++---- tasks/scan/scan_rfo.html | 178 +++++++++++++++--------- tasks/scan/scan_sd.html | 248 +++++++++++++++++++++++++++++++++ tasks/scan/scan_sdcg.html | 266 ++++++++++++++++++++++++++++++++++++ tasks/singlepoint.html | 5 + tasks/ts/ts.html | 5 + tasks/ts/ts_autoneb.html | 5 + tasks/ts/ts_dimmer.html | 5 + tasks/ts/ts_neb.html | 5 + tasks/ts/ts_prfo.html | 5 + tasks/ts/ts_string.html | 5 + tutorials/input_output.html | 27 ++-- tutorials/installation.html | 15 +- tutorials/quickstart.html | 15 +- 42 files changed, 1282 insertions(+), 255 deletions(-) create mode 100644 tasks/scan/scan_cg.html create mode 100644 tasks/scan/scan_sd.html create mode 100644 tasks/scan/scan_sdcg.html diff --git a/development.html b/development.html index e26c861..a8ceacc 100644 --- a/development.html +++ b/development.html @@ -71,7 +71,7 @@

Version 0.1.0 — December 31, 2025
  • Geometry optimization — L-BFGS, RFO, steepest descent, conjugate gradient, DIIS, and bracketing L-BFGS methods.
  • Transition state search — NEB, CI-NEB, P-RFO, Dimer, and Growing String methods.
  • IRC — Intrinsic reaction coordinate with GS, LQA, HPC, and EulerPC integrators.
    • -
  • PES scan — 1D relaxed and rigid scans along bonds, angles, and dihedrals.
    • +
  • PES scan — 1D, 2D, and 3D relaxed or rigid scans along bonds, angles, and dihedrals.
  • Solvation — GBSA implicit solvation and explicit solvent models.
  • Constraints — Fix atoms, bonds, angles, and dihedral angles during optimization.
  • GPU acceleration — Full CUDA support for all ML potential evaluations.
    • diff --git a/downloads.html b/downloads.html index ed18474..6ea16e9 100644 --- a/downloads.html +++ b/downloads.html @@ -38,9 +38,10 @@

    Downloads

    Source Code

    -

    MAPLE is hosted on GitHub. Clone the repository to get the latest development version (see the license terms below).

    +

    MAPLE is hosted on GitHub. Clone the public source repository for the published code line (see the license terms below).

    Source Code on GitHub →

    git clone https://github.com/ClickFF/MAPLE.git
    +

    Documentation note: The SCAN method pages are synchronized with the MAPLE debug/OPT development snapshot verified at commit 85a39ca. The public upstream link may lag until those changes are merged.

    Installation

    Follow the step-by-step guide to set up Python, PyTorch, and the ML potential dependencies.

    diff --git a/functions/constrain.html b/functions/constrain.html index 766a9af..7c6a776 100644 --- a/functions/constrain.html +++ b/functions/constrain.html @@ -75,6 +75,8 @@
  • L-BFGS
  • RFO
  • SD
    • +
  • CG
    • +
  • SD/CG
  • @@ -92,6 +94,9 @@
  • @@ -225,7 +230,7 @@

    Dihedral Constraints (D Command)

    Scan Coordinates (S Command)

    -

    The S command defines an internal coordinate to be scanned over a range of values. It is used exclusively with #scan tasks. The scan systematically varies the specified coordinate from its initial value, stepping by a fixed increment for a given number of steps. At each step, the remaining degrees of freedom are optimized.

    +

    The S command defines an internal coordinate to be scanned over a range of values. It is used exclusively with #scan tasks. The scan systematically varies the specified coordinate from its initial value, stepping by a fixed increment for the requested number of steps. Relaxed scans optimize the remaining degrees of freedom at each scan point; rigid scans move the detected connected fragment to satisfy the target coordinate without optimization.

    @@ -254,17 +259,17 @@

    Scan Coordinates (S Command)

    -

    The step parameter specifies the increment per step (in Angstroms for bond lengths, degrees for angles), and nsteps is the number of steps to take.

    +

    The step parameter specifies the increment per step (in Angstroms for bond lengths, degrees for angles and dihedrals). MAPLE writes the initial point plus each requested step, so one S line produces nsteps + 1 scan points.

    S 1 2 0.05 10
    -

    This scans the bond length between atoms 1 and 2, increasing it by 0.05 Angstroms at each of 10 steps.

    +

    This scans the bond length between atoms 1 and 2 over 11 points: the initial geometry plus 10 increments of 0.05 Angstroms.

    S 2 1 3 10.0 6
    -

    This scans the bond angle at atom 1 (between atoms 2, 1, and 3), increasing it by 10 degrees at each of 6 steps.

    +

    This scans the bond angle at atom 1 (between atoms 2, 1, and 3) over 7 points: the initial angle plus 6 increments of 10 degrees.

    Tip

    -

    You can define multiple S commands to perform a multi-dimensional scan. MAPLE will systematically vary all scan coordinates, creating a grid of geometries across the combined coordinate space.

    +

    You can define up to three S commands for 1D, 2D, or 3D scans. MAPLE varies all scan coordinates as a Cartesian-product grid across the combined coordinate space.

    POST Command

    @@ -325,36 +330,23 @@

    Constrained optimization: fix a dihedral angle

    The dihedral angle along H(5)-C(1)-C(2)-C(3) is fixed at its initial value while the rest of the geometry relaxes.

    1D bond scan

    - 
    #model = uma
-#device = gpu0
-#scan(method=lbfgs)
-
-0 1
-C    0.000000    0.000000    0.000000
-C    1.540000    0.000000    0.000000
-H   -0.392000    1.011000    0.000000
-H   -0.392000   -0.506000    0.875000
-H   -0.392000   -0.506000   -0.875000
-H    1.932000    0.506000    0.875000
-H    1.932000    0.506000   -0.875000
-H    1.932000   -1.011000    0.000000
-
-S 1 2 0.05 10
    -

    Scans the C-C bond in 10 increments of 0.05 Angstroms.

    - -

    2D scan: bond length + bond angle

    - 
    #model = uma
-#device = gpu0
-#scan(method=lbfgs)
-
-0 1
-O    0.000000    0.000000    0.117300
-H    0.000000    0.757160   -0.469200
-H    0.000000   -0.757160   -0.469200
-
-S 1 2 0.05 5
-S 2 1 3 5.0 6
    -

    Simultaneously scans the O-H bond length (5 steps of 0.05 Angstroms) and the H-O-H bond angle (6 steps of 5 degrees), producing a 2D potential energy surface.

    +

    Checked-in MAPLE example: example/scan/C18.inp. The full coordinate block is kept in the source example; the real scan-defining lines are:

    + 
    #model=aimnet2nse
+#scan(mode=rigid)
+#device=gpu0
+
+S 1 36 0.1 50
    +

    Scans the atom 1–36 distance over 51 points: the initial geometry plus 50 increments of 0.1 Angstroms.

    + +

    2D scan: two distance coordinates

    +

    Checked-in MAPLE example: example/scan/da.inp. It defines a two-coordinate relaxed scan with the default L-BFGS method:

    + 
    #model=ANI-1xnr
+#scan
+#device=gpu0
+
+S 11 52 -0.1 15
+S 14 51 -0.1 15
    +

    Each coordinate gives 16 values, producing a 256-point 2D potential energy surface.

    Using the POST command for external constraints

    #model = uma
diff --git a/functions/solvent.html b/functions/solvent.html
index e3d72bf..6afb803 100644
--- a/functions/solvent.html
+++ b/functions/solvent.html
@@ -75,6 +75,8 @@
                     
  • L-BFGS
    • 
                     
  • RFO
    • 
                     
  • SD
    • 
+                    
  • CG
    • 
+                    
  • SD/CG
    •
  • @@ -92,6 +94,9 @@
  • diff --git a/general.html b/general.html index 6afd9e0..6377cd8 100644 --- a/general.html +++ b/general.html @@ -126,7 +126,7 @@

    Transition State

    scan

    PES Scan

    -

    1D to N-dimensional relaxed or rigid scans along chosen internal coordinates.

    +

    1D, 2D, or 3D relaxed or rigid scans along chosen internal coordinates.
    irc
    diff --git a/home1.html b/home1.html index b6f974b..f9abac4 100644 --- a/home1.html +++ b/home1.html @@ -85,11 +85,13 @@

    Transition State Search

    II. Input Structure Requirements

    PES Scan

    -

    Sweeps selected bonds, angles, or dihedrals to build a relaxed potential-energy map along chosen coordinates.

    +

    Sweeps selected bonds, angles, or dihedrals to build 1D, 2D, or 3D relaxed/rigid potential-energy maps.

    I. Input Parameters

    → method: L-BFGS

    -

    I. Adjustable Parameters

    → method: RFO

    +

    → method: SD

    +

    → method: CG

    +

    → method: SD/CG

    I. Adjustable Parameters

    II. Output File Contents

    diff --git a/index.html b/index.html index 75dbe3c..e2cb26a 100644 --- a/index.html +++ b/index.html @@ -77,7 +77,7 @@

    Vibrational Analysis

    🗺️

    PES Scanning

    -

    1D to N-dimensional relaxed or rigid scans. Map energy landscapes along chosen coordinates.

    +

    1D, 2D, or 3D relaxed or rigid scans. Map energy landscapes along chosen coordinates.
    🌊
    diff --git a/setup/coordinates.html b/setup/coordinates.html index 4ee08c0..11208fa 100644 --- a/setup/coordinates.html +++ b/setup/coordinates.html @@ -75,6 +75,8 @@
  • L-BFGS
  • RFO
  • SD
    • +
  • CG
    • +
  • SD/CG
  • @@ -92,6 +94,9 @@
  • @@ -268,20 +273,14 @@

    Example with constraints

    In this example, atom 3 (oxygen) is frozen in place and the bond between atoms 1 and 2 (C-C) is constrained at its initial distance during optimization.

    Example with scan coordinate

    - 
    #model = uma
-#scan(method=lbfgs)
-
-0 1
-C    0.000000    0.000000    0.000000
-C    1.540000    0.000000    0.000000
-H   -0.392000    1.011000    0.000000
-H   -0.392000   -0.506000    0.875000
-H    1.932000    0.506000    0.875000
-H    1.932000   -1.011000    0.000000
+        
    Checked-in MAPLE example: example/scan/C18.inp. The full C18 coordinates are in that file; the real task header and scan coordinate are:
    
+        
    #model=aimnet2nse
+#scan(mode=rigid)
+#device=gpu0
 
-S 1 2 0.05 10
    
+S 1 36 0.1 50
    -

    This scans the C-C bond length (atoms 1 and 2) in 10 steps of 0.05 Angstroms each.

    +

    This scans the distance between atoms 1 and 36 over 51 points: the initial geometry plus 50 increments of 0.1 Angstroms.