diff --git a/about.html b/about.html index f86b579..39893e3 100644 --- a/about.html +++ b/about.html @@ -5,6 +5,7 @@ About MAPLE +
@@ -17,7 +18,7 @@
  • @@ -92,6 +95,9 @@
  • @@ -225,7 +231,7 @@

    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 +260,17 @@

    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

    @@ -285,7 +291,7 @@

    Examples

    Constrained optimization: freeze atoms and fix a bond

    #model = uma
     #device = gpu0
    -#opt(method=lbfgs, convergence=tight)
    +#opt(method=lbfgs, level=tight)
     
     0 1
     C    0.000000    0.000000    0.000000
    @@ -325,36 +331,27 @@ 

    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)
    +        

    Checked-in MAPLE example: example/scan/C18.inp. The full coordinate block is kept in the source example; the scan command belongs after that coordinate block:

    +
    #model=aimnet2nse
    +#scan(mode=rigid)
    +#device=gpu0
     
    -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
    +[XYZ coordinates from example/scan/C18.inp]
     
    -S 1 2 0.05 10
    -

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

    +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: bond length + bond angle

    -
    #model = uma
    -#device = gpu0
    -#scan(method=lbfgs)
    +        

    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. The long coordinate block is omitted here, but the S commands must remain after it:

    +
    #model=ANI-1xnr
    +#scan
    +#device=gpu0
     
    -0 1
    -O    0.000000    0.000000    0.117300
    -H    0.000000    0.757160   -0.469200
    -H    0.000000   -0.757160   -0.469200
    +[XYZ coordinates from example/scan/da.inp]
     
    -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.

    +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..3699795 100644
    --- a/functions/solvent.html
    +++ b/functions/solvent.html
    @@ -5,6 +5,7 @@
       
       Solvation - MAPLE Documentation
       
    +  
     
     
       
    @@ -75,6 +76,8 @@
  • L-BFGS
  • RFO
  • SD
  • +
  • CG
  • +
  • SD/CG
  • @@ -92,6 +95,9 @@
  • @@ -262,7 +268,7 @@

    Usage Example

    #model = uma
     #device = gpu0
     #solv(implicit=gbsa)
    -#opt(method=lbfgs, convergence=tight)
    +#opt(method=lbfgs, level=tight)
     
     0 1
     C    0.000000    0.000000    0.000000
    @@ -278,7 +284,7 @@ 

    Usage Example

    #model = uma
     #device = gpu0
     #solv(explicit=water, radius=10.0, clash_cutoff=1.5, fix_dis=8.0)
    -#opt(method=lbfgs, convergence=medium)
    +#opt(method=lbfgs, level=medium)
     
     0 1
     C    0.000000    0.000000    0.000000
    diff --git a/general.html b/general.html
    index 6afd9e0..f732e47 100644
    --- a/general.html
    +++ b/general.html
    @@ -5,6 +5,7 @@
       
       About MAPLE — Machine-learning Potential for Landscape Exploration
       
    +  
     
     
       
    @@ -126,7 +127,7 @@

    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..12f0596 100644 --- a/home1.html +++ b/home1.html @@ -5,6 +5,7 @@ MAPLE User Guide +
    @@ -85,11 +86,13 @@

    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..0772566 100644 --- a/index.html +++ b/index.html @@ -5,6 +5,7 @@ MAPLE — Machine-learning Potential for Landscape Exploration +
    @@ -77,7 +78,7 @@

    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.

    🌊
    @@ -100,6 +101,10 @@

    More Coming Soon

  • @@ -92,6 +95,9 @@
  • @@ -168,7 +174,7 @@

    External XYZ Files

    For larger molecules or when reusing geometries across calculations, you can load coordinates from an external XYZ file using the XYZ keyword followed by the file path.

    #model = aimnet2
    -#opt(method=lbfgs, convergence=tight)
    +#opt(method=lbfgs, level=tight)
     
     XYZ /path/to/molecule.xyz
    @@ -268,20 +274,16 @@

    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)
    +        

    Checked-in MAPLE example: example/scan/C18.inp. The full C18 coordinates are in that file; the scan coordinate is a post-processing line after the coordinates:

    +
    #model=aimnet2nse
    +#scan(mode=rigid)
    +#device=gpu0
     
    -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
    +[XYZ coordinates from example/scan/C18.inp]
     
    -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.

  • @@ -92,6 +95,9 @@
  • diff --git a/setup/model_ani.html b/setup/model_ani.html index 7b0fe6d..7eab2e8 100644 --- a/setup/model_ani.html +++ b/setup/model_ani.html @@ -5,6 +5,7 @@ ANI Models - MAPLE Documentation +
    @@ -75,6 +76,8 @@
  • L-BFGS
  • RFO
  • SD
  • +
  • CG
  • +
  • SD/CG
  • @@ -92,6 +95,9 @@
  • @@ -203,7 +209,7 @@

    General organic optimization

    High-accuracy with coupled-cluster potential

    #model=ani1ccx
     #device=gpu0
    -#opt(method=lbfgs, convergence=extratight)
    +#opt(method=lbfgs, level=extratight)
     
     0 1
     O    0.000000    0.000000    0.117300
    @@ -214,7 +220,7 @@ 

    With D4 dispersion for non-covalent interactions

    #model=ani2x
     #d4
     #device=gpu0
    -#opt(method=lbfgs, convergence=tight)
    +#opt(method=lbfgs, level=tight)
     
     XYZ /path/to/dimer_complex.xyz
    diff --git a/setup/model_mace.html b/setup/model_mace.html index 6e106c0..d6a602c 100644 --- a/setup/model_mace.html +++ b/setup/model_mace.html @@ -5,6 +5,7 @@ MACE & EGRET - MAPLE Documentation +
    @@ -75,6 +76,8 @@
  • L-BFGS
  • RFO
  • SD
  • +
  • CG
  • +
  • SD/CG
  • @@ -92,6 +95,9 @@
  • @@ -199,14 +205,14 @@

    Usage Examples

    Quick screening with MACE-OFF23 Small

    #model=maceoff23s
     #device=gpu0
    -#opt(convergence=loose)
    +#opt(level=loose)
     
     XYZ /path/to/molecule.xyz

    Publication-quality optimization with MACE-OFF23 Large

    #model=maceoff23l
     #device=gpu0
    -#opt(method=lbfgs, convergence=tight)
    +#opt(method=lbfgs, level=tight)
     
     XYZ /path/to/optimized_guess.xyz
    @@ -220,7 +226,7 @@

    Frequency calculation

    CPU fallback for large systems

    #model=maceoff23s
     #device=cpu
    -#opt(convergence=loose)
    +#opt(level=loose)
     
     XYZ /path/to/large_system.xyz
    diff --git a/setup/model_uma.html b/setup/model_uma.html index 38f6972..c744270 100644 --- a/setup/model_uma.html +++ b/setup/model_uma.html @@ -5,6 +5,7 @@ UMA - MAPLE Documentation +
    @@ -75,6 +76,8 @@
  • L-BFGS
  • RFO
  • SD
  • +
  • CG
  • +
  • SD/CG
  • @@ -92,6 +95,9 @@
  • @@ -130,22 +136,25 @@

    UMA — Universal Models for Atoms

    UMA is a family of universal machine-learning interatomic potentials developed by Meta's FAIR Chemistry team. Trained on approximately 500 million unique 3D atomic structures spanning molecules, materials, and catalysts, UMA is designed to serve as a single universal model that handles diverse chemical domains without requiring fine-tuning.

    -

    MAPLE defaults to UMA v1.2 (uma-s-1p2), which offers ~50% faster inference and ~40% improved accuracy on molecular systems compared to v1.1.

    +

    MAPLE defaults to the small UMA v1.1 checkpoint (uma-s-1p1) for compatibility. You can explicitly select newer or larger checkpoints, and you can choose the FAIR Chemistry inference interface for speed-critical GPU workloads.

    Configuration

    -

    Basic usage with all defaults (task = omol, size = uma-s-1p2):

    +

    Basic usage with all defaults (task = inferred from the system, size = uma-s-1p1, inference = default):

    #model=uma

    Specify task and/or size explicitly:

    #model=uma(task=omat, size=uma-s-1p2)
    -

    Both parameters are optional and can be used independently:

    -
    # Only change task (size stays at default uma-s-1p2)
    +        

    The task, size, and inference parameters are optional and can be used independently:

    +
    # Only change task (size stays at default uma-s-1p1)
     #model=uma(task=oc20)
     
    -# Only change size (task stays at default omol)
    -#model=uma(size=uma-m-1p1)
    +# Only change size (task remains auto-selected) +#model=uma(size=uma-m-1p1) + +# Only change the FAIR Chemistry inference interface +#model=uma(inference=turbo)

    Model Sizes

    @@ -167,14 +176,14 @@

    Model Sizes

    v1.2 6.6M ~150M - Default. Latest and fastest; ~50% faster, ~40% more accurate than v1.1 + Latest and fastest; ~50% faster, ~40% more accurate than v1.1 on molecular benchmarks uma-s-1p1 v1.1 6.6M ~150M - Previous stable release; use if v1.2 compatibility issues arise + Default. Compatibility-first small checkpoint uma-m-1p1 @@ -188,7 +197,45 @@

    Model Sizes

    Tip

    -

    For most use cases, the default uma-s-1p2 provides the best balance of speed and accuracy. Switch to uma-m-1p1 when you need the highest possible accuracy and can tolerate slower evaluation.

    +

    The default uma-s-1p1 is the compatibility-first choice. Select uma-s-1p2 when you want the newer v1.2 checkpoint, or uma-m-1p1 when you need higher accuracy and can tolerate slower evaluation.

    +
    + +

    Inference Interface

    + +

    The inference option selects the FAIR Chemistry inference interface used by UMA. The MAPLE input keyword is inference; "interface" here describes the backend path being selected.

    + + + + + + + + + + + + + + + + + + + + + +
    ModeUse caseNotes
    defaultGeneral-purpose calculations and CPU runsDefault. Safest for short jobs and changing-composition workflows.
    turboCUDA runs with repeated fixed-composition evaluationsOpt-in fast path for workloads such as NEB, TS, and frequency calculations; short jobs may not recover the startup cost.
    + +
    # Explicitly request the CUDA turbo inference interface
    +#model=uma(inference=turbo)
    +#device=gpu0
    +
    +# Combine task, size, and inference options
    +#model=uma(task=omat, size=uma-s-1p2, inference=turbo)
    + +
    +

    Note

    +

    On CPU, MAPLE falls back to inference=default even if turbo is requested, because the turbo path depends on CUDA-oriented FAIR Chemistry kernels.

    Task Domains

    @@ -274,7 +321,7 @@

    Charge and Spin

    Usage Examples

    Default: molecular geometry optimization

    -
    # Default: uma-s-1p2 checkpoint, omol task
    +        
    # Default: uma-s-1p1 checkpoint, omol task for this molecular system
     #model=uma
     #device=gpu0
     #opt(method=lbfgs)
    @@ -333,6 +380,7 @@ 

    Compatibility Notes

  • D4 dispersion: Not supported with UMA. The model's training data already includes dispersion-corrected DFT for relevant tasks (PBE+D3 for omc, odac, oc25).
  • GBSA solvation: Fully supported. QEq charges are computed automatically when implicit solvation is enabled.
  • All MAPLE job types are compatible with UMA: single point, optimization, transition state search, IRC, frequency, PES scan, and molecular dynamics.
  • +
  • UMA inference interface: use inference=turbo only when you explicitly want the CUDA fast path; otherwise keep the default interface.
  • Requires fairchem-core Python package (v2.9+) and a HuggingFace account with access to the facebook/UMA repository.
  • @@ -349,6 +397,7 @@

    On this page

  • @@ -92,6 +95,9 @@
  • @@ -214,7 +220,7 @@

    Available Models

    UMA uma Broad periodic table coverage (83+ elements) - Universal model from Meta FAIR (v1.2); supports 7 task domains, 3 model sizes. Details → + Universal model from Meta FAIR; supports 7 task domains, 3 model sizes, and inference=default|turbo. Details → @@ -261,11 +267,11 @@

    Usage Examples

    Below are complete input file examples demonstrating model selection for various scenarios.

    -

    General-purpose optimization with UMA (default: v1.2, omol task)

    -
    # Uses uma-s-1p2 checkpoint, omol task by default
    +        

    General-purpose optimization with UMA (default: small v1.1 checkpoint, omol task)

    +
    # Uses uma-s-1p1 checkpoint and default inference interface
     #model=uma
     #device=gpu0
    -#opt(method=lbfgs, convergence=tight)
    +#opt(method=lbfgs, level=tight)
     
     0 1
     C    0.000000    0.000000    0.000000
    @@ -280,11 +286,21 @@ 

    UMA for inorganic materials (omat task)

    XYZ /path/to/material.xyz
    +

    UMA with CUDA turbo inference

    +
    # Opt in to the FAIR Chemistry turbo inference interface for repeated GPU evaluations
    +#model=uma(inference=turbo)
    +#device=gpu0
    +#ts(method=neb)
    +
    +XYZ /path/to/reactant.xyz
    +
    +XYZ /path/to/product.xyz
    +

    High-accuracy calculation with AIMNet2 and D4

    #model = aimnet2
     #d4
     #device = gpu0
    -#opt(method=lbfgs, convergence=extratight)
    +#opt(method=lbfgs, level=extratight)
     
     0 1
     C    0.000000    0.000000    0.000000
    @@ -303,7 +319,7 @@ 

    Frequency calculation with MACE-OFF23

    CPU-based calculation for large systems

    #model = maceoff23s
     #device = cpu
    -#opt(convergence=loose)
    +#opt(level=loose)
     
     XYZ /path/to/large_molecule.xyz
    diff --git a/setup/settings.html b/setup/settings.html index 765c481..4569647 100644 --- a/setup/settings.html +++ b/setup/settings.html @@ -5,6 +5,7 @@ Settings - MAPLE Documentation +
    @@ -75,6 +76,8 @@
  • L-BFGS
  • RFO
  • SD
  • +
  • CG
  • +
  • SD/CG
  • @@ -92,6 +95,9 @@
  • @@ -147,16 +153,16 @@

    #model

    #model = maceoff23m

    #opt

    -

    Requests a geometry optimization. Parameters such as the optimization method and convergence criteria can be supplied in parentheses.

    +

    Requests a geometry optimization. Parameters such as the optimization method and convergence level can be supplied in parentheses.

    #opt
     #opt(method=lbfgs)
    -#opt(method=lbfgs, convergence=tight)
    +#opt(method=lbfgs, level=tight)

    #ts

    -

    Requests a transition state search. The method and convergence settings are specified in parentheses.

    +

    Requests a transition state search. The method and convergence level are specified in parentheses.

    #ts
     #ts(method=prfo)
    -#ts(method=neb, convergence=tight)
    +#ts(method=neb, level=tight)

    #freq

    Requests a vibrational frequency calculation. This computes the Hessian matrix and derives harmonic frequencies, zero-point energy, and thermochemical properties.

    @@ -169,10 +175,12 @@

    #irc

    #irc(method=lqa, steps=50)

    #scan

    -

    Requests a potential energy surface (PES) scan along one or more internal coordinates. Scan coordinates are defined in the post-processing section of the input file.

    +

    Requests a potential energy surface (PES) scan along one to three internal coordinates. Scan coordinates are defined in the post-processing section of the input file.

    #scan
    -#scan(method=lbfgs)
    -#scan(method=rfo, convergence=tight)
    +#scan(mode=rigid) +#scan(method=lbfgs, mode=relaxed, level=tight) +#scan(method=rfo, mode=relaxed, level=tight) +

    Current runtime support: relaxed scans reuse the optimization dispatcher and support lbfgs, rfo, sd, cg, and sdcg. Rigid scans bypass optimization and ignore optimizer settings.

    #device

    Specifies the hardware device on which the calculation will run. See Device Selection below for details.

    @@ -276,7 +284,7 @@

    Device Selection

    Convergence Levels

    -

    MAPLE provides several predefined convergence levels for geometry optimizations and transition state searches. These control the thresholds for maximum force (f_max), RMS force (f_rms), maximum displacement (dp_max), and RMS displacement (dp_rms). All force values are in Hartree/Bohr and displacements in Bohr.

    +

    MAPLE provides several predefined convergence levels for geometry optimizations and transition state searches. These control the thresholds for maximum force (f_max), RMS force (f_rms), maximum displacement (dp_max), and RMS displacement (dp_rms). Force thresholds are in Hartree/Angstrom and displacement thresholds are in Angstrom.

    @@ -291,52 +299,52 @@

    Convergence Levels

    - - - - + + + + - - - - + + + + - - - - + + + + - - - - + + + + - - - - + + + + - - - - + + + +
    extratight1.5e-061.0e-066.0e-064.0e-063.0e-042.0e-043.0e-042.0e-04
    tight1.5e-051.0e-056.0e-054.0e-058.5e-045.5e-041.1e-037.5e-04
    medium4.5e-043.0e-041.8e-031.2e-032.85e-031.90e-033.15e-032.10e-03
    loose2.5e-031.7e-031.0e-026.7e-033.80e-032.50e-036.00e-034.00e-03
    extraloose2.5e-021.7e-021.0e-016.7e-027.55e-035.00e-031.20e-028.00e-03
    superloose2.5e-011.7e-011.0e+006.7e-018.50e-025.50e-021.45e-019.50e-02

    Set the convergence level inside the task command parentheses:

    -
    #opt(method=lbfgs, convergence=tight)
    -#ts(method=prfo, convergence=extratight)
    +
    #opt(method=lbfgs, level=tight)
    +#ts(method=prfo, level=extratight)

    Tip

    diff --git a/tasks/frequency.html b/tasks/frequency.html index 021367b..1a11530 100644 --- a/tasks/frequency.html +++ b/tasks/frequency.html @@ -5,6 +5,7 @@ Vibrational Frequency Analysis - MAPLE +
    @@ -75,6 +76,8 @@
  • L-BFGS
  • RFO
  • SD
  • +
  • CG
  • +
  • SD/CG
  • @@ -92,6 +95,9 @@
  • diff --git a/tasks/irc/irc.html b/tasks/irc/irc.html index e4ab612..da1a0d2 100644 --- a/tasks/irc/irc.html +++ b/tasks/irc/irc.html @@ -5,6 +5,7 @@ Intrinsic Reaction Coordinate (IRC) - MAPLE +
    @@ -75,6 +76,8 @@
  • L-BFGS
  • RFO
  • SD
  • +
  • CG
  • +
  • SD/CG
  • @@ -92,6 +95,9 @@
  • @@ -260,7 +266,7 @@

    Workflow

    diff --git a/tasks/irc/irc_eulerpc.html b/tasks/irc/irc_eulerpc.html index 818f9d7..280727d 100644 --- a/tasks/irc/irc_eulerpc.html +++ b/tasks/irc/irc_eulerpc.html @@ -5,6 +5,7 @@ IRC: Euler Predictor-Corrector (EulerPC) - MAPLE +