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Compared outputs of NWChem versions #5

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Output comparison of different NWChem versions
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9 changes: 4 additions & 5 deletions Python/lib/NWChem_Wrapper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,8 +22,8 @@
. goToLine()
. findNextOccurrence()

Last edit: 2026-04-09
Author: Dinis Abranches, Fathya Salih, Ching Ting Leung
Last edit: 2025-01-29
Author: Dinis Abranches, Fathya Salih
"""

# =============================================================================
Expand Down Expand Up @@ -254,7 +254,6 @@ def readOutput(outputPath,doCOSMO=True):
# Set COSMO-related outputs to None
surfaceArea=None
segmentAreas=None
segAtoms=None
# Skip three lines
for __ in range(3): file.readline()
# Retrieve final coordinates
Expand Down Expand Up @@ -508,9 +507,9 @@ def goToLine(file,lineNumber):
None.

"""

# Rewind file
file.seek(0)

# Initiate loop
for __ in range(lineNumber+1):
file.readline()
# Output
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10 changes: 10 additions & 0 deletions README.md
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Expand Up @@ -60,6 +60,16 @@ Use these instructions if you already have NWChem installed, if you need a custo
./run-tests.sh
```



## Comparison of NWChem Versions

The `sp-compare/` folder contains outputs from different versions of NWChem for methane calculations. This includes results from various NWChem versions to compare consistency and differences in sigma profile generation.

A summary of the differences is provided in `sp-compare/comparison_Methane.md`.



## Usage Instructions

**Simple usage example**:
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158 changes: 158 additions & 0 deletions sp-compare/comparison_Methane.md
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# NWChem Comparison Report

**Date:** 2026-05-12
**Molecule:** SP-NoInitXYZ-Mol_Methane
**Reference variant:** nw720_ks (Version of output in manuscript)
**Author:** Ching Ting Leung

## Files Compared

| Variant | N Atoms | N Segments | Surface Area (Ų) | Status |
|---|---|---|---|---|
| nw720_ks | 5 | 248 | 49.6460 | OK |
| nw720_yk | 5 | 289 | 55.3860 | OK |
| nw723_ks | 5 | 248 | 49.6460 | OK |
| nw723_yk | 5 | 289 | 55.3860 | OK |
| nw73_ks | 5 | 429 | 55.2840 | OK |
| nw73_yk | 5 | 289 | 55.3860 | OK |


- **nw720_ks**: `sp-compare/nw720_ks/SP-NoInitXYZ-Mol_Methane/SP-NoInitXYZ-Mol_Methane_0/output.nw`
- **nw720_yk**: `sp-compare/nw720_yk/SP-NoInitXYZ-Mol_Methane/SP-NoInitXYZ-Mol_Methane_0/output.nw`
- **nw723_ks**: `sp-compare/nw723_ks/SP-NoInitXYZ-Mol_Methane/SP-NoInitXYZ-Mol_Methane_0/output.nw`
- **nw723_yk**: `sp-compare/nw723_yk/SP-NoInitXYZ-Mol_Methane/SP-NoInitXYZ-Mol_Methane_0/output.nw`
- **nw73_ks**: `sp-compare/nw73_ks/SP-NoInitXYZ-Mol_Methane/SP-NoInitXYZ-Mol_Methane_0/output.nw`
- **nw73_yk**: `sp-compare/nw73_yk/SP-NoInitXYZ-Mol_Methane/SP-NoInitXYZ-Mol_Methane_0/output.nw`


## Surface Area (Ų)

| Variant | Surface Area (Ų) |
|---|---|
| nw720_ks | 49.646000 |
| nw720_yk | 55.386000 |
| nw723_ks | 49.646000 |
| nw723_yk | 55.386000 |
| nw73_ks | 55.284000 |
| nw73_yk | 55.386000 |

| Comparison | Absolute Diff (Ų) | Relative Diff |
|---|---|---|
| nw720_yk − nw720_ks | +5.740000 | +11.5619% |
| nw723_ks − nw720_ks | +0.000000 | +0.0000% |
| nw723_yk − nw720_ks | +5.740000 | +11.5619% |
| nw73_ks − nw720_ks | +5.638000 | +11.3564% |
| nw73_yk − nw720_ks | +5.740000 | +11.5619% |

## Number of Surface Segments

| Variant | N Segments |
|---|---|
| nw720_ks | 248 |
| nw720_yk | 289 |
| nw723_ks | 248 |
| nw723_yk | 289 |
| nw73_ks | 429 |
| nw73_yk | 289 |

## Segment Areas (a.u.²)

| Variant | Mean | Std | Min | Max |
|---|---|---|---|---|
| nw720_ks | 0.714866 | 0.390272 | 0.148120 | 1.402350 |
| nw720_yk | 0.684386 | 0.454716 | 0.000063 | 1.402354 |
| nw723_ks | 0.714866 | 0.390272 | 0.148120 | 1.402350 |
| nw723_yk | 0.684386 | 0.454716 | 0.000063 | 1.402354 |
| nw73_ks | 0.460197 | 0.200621 | 0.316000 | 0.747920 |
| nw73_yk | 0.684386 | 0.454716 | 0.000063 | 1.402354 |

> **Note:** Segment counts differ across variants — only aggregate statistics are shown.

## Segment–Atom Assignments

> **Note:** Atom-index column not present in the segment table for the following variants (2-column output format). Segment–atom assignments are unavailable: `nw720_yk`, `nw723_yk`, `nw73_yk`

Number of surface segments assigned to each atom index:

| Variant | Atom 1 | Atom 2 | Atom 3 | Atom 4 | Atom 5 |
|---|---|---|---|---|---|
| nw720_ks | 89 | 39 | 42 | 39 | 39 |
| nw723_ks | 89 | 39 | 42 | 39 | 39 |
| nw73_ks | 143 | 74 | 66 | 71 | 75 |

## Final Atom Coordinates

**Reference:** nw720_ks — 5 atoms: C, H, H, H, H

### nw720_yk vs nw720_ks

- **Max displacement:** 0.000109 Å (atom 3: H)
- **Mean displacement:** 0.000077 Å

| Atom | Element | Δ (Å) | ref (nw720_ks) | variant (nw720_yk) |
|---|---|---|---|---|
| 1 | C | 0.000061 | (-0.0001, 0.0000, 0.0000) | (-0.0000, -0.0000, 0.0000) |
| 2 | H | 0.000077 | (-0.6624, -0.8498, -0.1721) | (-0.6624, -0.8497, -0.1721) |
| 3 | H | 0.000109 | (-0.4471, 0.9012, -0.4223) | (-0.4472, 0.9012, -0.4222) |
| 4 | H | 0.000065 | (0.1469, 0.1351, 1.0727) | (0.1469, 0.1352, 1.0727) |
| 5 | H | 0.000075 | (0.9627, -0.1866, -0.4783) | (0.9627, -0.1866, -0.4783) |

### nw723_ks vs nw720_ks

- **Max displacement:** 0.000000 Å (atom 1: C)
- **Mean displacement:** 0.000000 Å

| Atom | Element | Δ (Å) | ref (nw720_ks) | variant (nw723_ks) |
|---|---|---|---|---|
| 1 | C | 0.000000 | (-0.0001, 0.0000, 0.0000) | (-0.0001, 0.0000, 0.0000) |
| 2 | H | 0.000000 | (-0.6624, -0.8498, -0.1721) | (-0.6624, -0.8498, -0.1721) |
| 3 | H | 0.000000 | (-0.4471, 0.9012, -0.4223) | (-0.4471, 0.9012, -0.4223) |
| 4 | H | 0.000000 | (0.1469, 0.1351, 1.0727) | (0.1469, 0.1351, 1.0727) |
| 5 | H | 0.000000 | (0.9627, -0.1866, -0.4783) | (0.9627, -0.1866, -0.4783) |

### nw723_yk vs nw720_ks

- **Max displacement:** 0.000109 Å (atom 3: H)
- **Mean displacement:** 0.000077 Å

| Atom | Element | Δ (Å) | ref (nw720_ks) | variant (nw723_yk) |
|---|---|---|---|---|
| 1 | C | 0.000061 | (-0.0001, 0.0000, 0.0000) | (-0.0000, -0.0000, 0.0000) |
| 2 | H | 0.000077 | (-0.6624, -0.8498, -0.1721) | (-0.6624, -0.8497, -0.1721) |
| 3 | H | 0.000109 | (-0.4471, 0.9012, -0.4223) | (-0.4472, 0.9012, -0.4222) |
| 4 | H | 0.000065 | (0.1469, 0.1351, 1.0727) | (0.1469, 0.1352, 1.0727) |
| 5 | H | 0.000075 | (0.9627, -0.1866, -0.4783) | (0.9627, -0.1866, -0.4783) |

### nw73_ks vs nw720_ks

- **Max displacement:** 0.000127 Å (atom 3: H)
- **Mean displacement:** 0.000092 Å

| Atom | Element | Δ (Å) | ref (nw720_ks) | variant (nw73_ks) |
|---|---|---|---|---|
| 1 | C | 0.000070 | (-0.0001, 0.0000, 0.0000) | (-0.0000, 0.0000, -0.0000) |
| 2 | H | 0.000098 | (-0.6624, -0.8498, -0.1721) | (-0.6624, -0.8497, -0.1721) |
| 3 | H | 0.000127 | (-0.4471, 0.9012, -0.4223) | (-0.4473, 0.9012, -0.4222) |
| 4 | H | 0.000062 | (0.1469, 0.1351, 1.0727) | (0.1470, 0.1351, 1.0727) |
| 5 | H | 0.000102 | (0.9627, -0.1866, -0.4783) | (0.9627, -0.1866, -0.4783) |

### nw73_yk vs nw720_ks

- **Max displacement:** 0.000109 Å (atom 3: H)
- **Mean displacement:** 0.000077 Å

| Atom | Element | Δ (Å) | ref (nw720_ks) | variant (nw73_yk) |
|---|---|---|---|---|
| 1 | C | 0.000061 | (-0.0001, 0.0000, 0.0000) | (-0.0000, -0.0000, 0.0000) |
| 2 | H | 0.000077 | (-0.6624, -0.8498, -0.1721) | (-0.6624, -0.8497, -0.1721) |
| 3 | H | 0.000109 | (-0.4471, 0.9012, -0.4223) | (-0.4472, 0.9012, -0.4222) |
| 4 | H | 0.000065 | (0.1469, 0.1351, 1.0727) | (0.1469, 0.1352, 1.0727) |
| 5 | H | 0.000075 | (0.9627, -0.1866, -0.4783) | (0.9627, -0.1866, -0.4783) |

## Abbreviations
nw720: NWChem version 7.2.0
nw730: NWChem version 7.2.3
nw73: NWChem version 7.3.0
ks: COSMO KS (Klamt–Schüürmann) Model
yk: COSMO YK (York–Karplus) Model

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