MOMAP Skill (v2 — 2024A Verified)

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silico-quantum 3 1 Updated 1mo ago

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npx skillscat add silico-quantum/quantum-chem-skills/momap

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SKILL.md

MOMAP Skill (v2 — 2024A Verified)

MOMAP (Molecular Materials Property Prediction Package) — 分子材料光物理/传输性质预测
Version 2024A (2.3.7), Hongzhiwei Technology / Z.G. Shuai Group

Server Setup

# On marcus / marcus2
source /opt/MOMAP-2024A/env.sh
# or
module load momap/2024A-openmpi

Key env vars set by env.sh:

MOMAP_ROOT=/opt/MOMAP-2024A
MOMAP_BIN=/opt/MOMAP-2024A/bin
MOMAP_MPI_BIN=/opt/MOMAP-2024A/bin/openmpi/bin
MOMAP_LICENSE=/opt/MOMAP-2024A/license/hzwtech.lic
LD_LIBRARY_PATH includes .../openmpi/lib and .../lib

MPI compatibility note: MOMAP ships OpenMPI 1.x but the system OpenMPI is 3.1.4.
The -machinefile flag is not supported in OpenMPI 3.x (use --hostfile).
→ Copy and patch momap script: sed 's/-machinefile/--hostfile/g'
→ Run python momap_patched -i momap.inp
→ Nodefile format for 3.x: localhost slots=4

Real Input Format (MOMAP 2024A)

No &control block, no jobtype. Each calculation type is a top-level flag + a named block.

Step 1: Electron-Vibration Coupling (EVC)

Prerequisites: Gaussian .log AND .fchk files for both states.
Generate .fchk with: formchk job.chk job.fchk

do_evc = 1

&evc
  ffreq(1) = "mol-s0.log"    # Ground state freq (S0)
  ffreq(2) = "mol-s1.log"    # Excited state freq (S1/T1)
  ftdipd   = "mol-s1.log"    # Optional: transition dipole from this file
  sort_mode = 1              # Mode sorting (1=default)
/

momap -i momap.inp

Output files:

File	Content
`evc.cart.dat`	Duschinsky matrix + Huang-Rhys factors (Cartesian)
`evc.dint.dat`	Duschinsky matrix (internal coords)
`evc.cart.abs`	Absorption data
`evc.dint.abs`	Absorption (internal coords)
`evc.out`	Full log with frequencies, mode pairing, reorganization energies
`evc.vib*.xyz`	Vibration mode visualizations
`evc.dx.x.xyz`	Displacement vectors
`evc.dx.x.com`	Displaced structure (Gaussian input)

Step 2: Spectrum (spec_tvcf)

do_spec_tvcf_ft   = 1       # Fourier transform of time correlation function
do_spec_tvcf_spec = 1       # Generate spectrum

&spec_tvcf
  DUSHIN   = .t.            # Use Duschinsky rotation
  HERZ     = .t.            # Herzberg-Teller effect (optional)
  Temp     = 300 K
  tmax     = 5000 fs        # Correlation time
  dt       = 0.001 fs        # Time step
  Ead      = 0.07509 au     # ⚠️ Adiabatic excitation energy (S1_min - S0_min)
  EDMA     = 0.92694 debye  # ⚠️ Absorption transition dipole (vertical)
  EDME     = 0.64751 debye  # ⚠️ Emission transition dipole (from S1 min)
  FreqScale = 1.0
  DSFile   = "evc.cart.dat" # From EVC step
  Emax     = 0.3 au         # Max energy for output
  dE       = 0.00001 au     # Energy resolution
  logFile  = "spec.tvcf.log"
  FtFile   = "spec.tvcf.ft.dat"
  FoFile   = "spec.tvcf.fo.dat"
  FoSFile  = "spec.tvcf.spec.dat"
/

momap -i momap.inp

Output (spec.tvcf.spec.dat):

#1Energy(Hartree) 2Energy(eV) 3Wavenumber(cm-1) 4Wavelength(nm) 5FC_abs 6FC_emi 7FC_emi_intensity

Step 3: ISC Rate (isc_tvcf)

do_isc_tvcf_ft   = 1       # Fourier transform
do_isc_tvcf_spec = 1       # Phosphorescence spectrum

&isc_tvcf
  DUSHIN   = .t.
  Temp     = 298 K
  tmax     = 5000 fs
  dt       = 0.001 fs
  Ead      = 0.094 au     # S1-T1 adiabatic gap
  Hso      = 116.9 cm-1   # ⚠️ Spin-orbit coupling (from PySOC or exp.)
  DSFile   = "evc.cart.dat"
  Emax     = 0.3 au
  logFile  = "isc.tvcf.log"
  FtFile   = "isc.tvcf.ft.dat"
  FoFile   = "isc.tvcf.fo.dat"
/

Output: ISC rate (k_ISC), phosphorescence spectrum.

Step 4: Internal Conversion (ic_tvcf)

do_ic_tvcf_ft   = 1
do_ic_tvcf_spec = 1

&ic_tvcf
  DUSHIN   = .t.
  Temp     = 300 K
  tmax     = 655 fs
  dt       = 0.01 fs
  Ead      = 0.094 au
  DSFile   = "evc.cart.dat"
  CoulFile = "evc.cart.nac"  # ⚠️ Non-adiabatic coupling
  logFile  = "ic.tvcf.log"
  FtFile   = "ic.tvcf.ft.dat"
/

Output: IC rate (k_IC) — non-radiative decay S₁→S₀.

Step 5: Spin-Orbit Coupling (PySOC)

Auto-generates SOC matrix elements from TDDFT:

do_pysoc = 1

&pysoc
  sched_type = local
  qc_exe     = g16
  qc_ppn     = 8
  pysoc_QM_code = 'gauss_tddft'
  n_excited_singlets = 4
  n_excited_triplets = 4
/

Output: Hso values (cm⁻¹) for S₁→T₁, S₁→T₂, ... → feeds into isc_tvcf.

Step 6: Full Rate Summary (spec_sums)

Sum-over-states method — computes k_r, k_IC, k_ISC simultaneously:

do_spec_sums = 1

&spec_sums
  DSFile     = "evc.cart.dat"
  Ead        = 0.094 au
  dipole_abs = 0.092 debye
  dipole_emi = 0.441 debye
  maxvib     = 10
  if_cal_ic  = .t.
  FWHM       = 500 cm-1
/

Output: All rates + quantum yield Φ in one pass.

Step 7: Charge Transport (transport)

Carrier mobility for OLED charge balance:

&transport
  do_transport_prepare              = 1
  do_transport_get_transferintegral = 1
  do_transport_get_re_evc           = 1
  do_transport_run_MC               = 1
  do_transport_get_mob_MC           = 1
  compute_engine  = 1            # Gaussian
  qc_exe          = g16
  basis_name      = b3lyp STO-3g
  temp            = 300
  ratetype        = marcus       # marcus or quanta
  lat_cutoff      = 4
  nsimu           = 2000
  tsimu           = 1000         # ns
  crystal         = molecule.cif
/

Output: Hole/electron mobility (cm²/V·s), transfer integrals, reorganization energies.

OLED TADF Design — Complete Workflow

       Gaussian                          MOMAP
  ┌──────────────┐              ┌─────────────────────┐
  │ S0 opt+freq  │──────┐       │ EVC (S₁→S₀)         │
  │ S1 opt+freq  │      ├──────→│ EVC (S₁→T₁)         │
  │ T1 opt+freq  │──────┘       │                     │
  │ NACT calc    │──→ NACME ──→│ ic_tvcf   → k_IC    │
  │ PySOC calc   │──→ Hso  ───→│ isc_tvcf  → k_ISC   │
  │ TDDFT (vert) │──→ EDMA/EDME│ spec_tvcf → k_r     │
  └──────────────┘              │ spec_sums → Φ (QY)  │
                                │ transport → μ_h, μ_e│
                                └─────────────────────┘

Key OLED figures of merit:

Quantity	MOMAP Module	Required Input
k_r (radiative)	spec_tvcf	EVC + EDMA/EDME
k_IC (internal conv.)	ic_tvcf	EVC + NACME
k_ISC (S₁→T₁)	isc_tvcf	EVC + Hso (SOC)
k_RISC (T₁→S₁)	isc_tvcf	k_ISC × exp(-ΔE_ST/kT)
Φ (quantum yield)	spec_sums	all above
μ_h (hole mobility)	transport	Transfer integral + λ
μ_e (electron mob.)	transport	Transfer integral + λ

Extracting Parameters from Gaussian Output

Ead (adiabatic excitation energy)

# From S0 log:
grep "SCF Done" s0.log | tail -1    →  E_SCF_S0

# From S1 log (last SCF Done = S1 min):
grep "SCF Done" s1.log | tail -1    →  E_SCF_S1

# Ead = E_SCF_S1 - E_SCF_S0  (in Hartree)

EDMA (absorption transition dipole moment)

From S0 geometry TDDFT output:

grep -A5 "transition electric dipole" s1.log | head -10
#  state    X        Y        Z       Dip.S.    Osc.
#    1   0.2169   0.2932   0.0000   0.1330    0.0079
# Dip.S. (au) → multiply by 2.5417 to convert to debye

EDME (emission transition dipole moment)

From S1 minimum geometry TDDFT (last Excited State block):

# Same as EDMA but from the last TDDFT block in s1.log
# Use Dip.S. of state 1 at S1-optimized geometry

Example: Azulene (bundled test)

Test directory: /opt/MOMAP-2024A/tests/azulene/gaussian/

mkdir ~/momap_azulene && cd ~/momap_azulene
# Copy ref log + fchk files
cp /opt/MOMAP-2024A/tests/azulene/gaussian/ref/azulene-s0.* .
cp /opt/MOMAP-2024A/tests/azulene/gaussian/ref/azulene-s1.* .

# Step 1: EVC
cat > momap_evc.inp << 'EOF'
do_evc = 1
&evc
  ffreq(1) = "azulene-s0.log"
  ffreq(2) = "azulene-s1.log"
/
EOF
source /opt/MOMAP-2024A/env.sh
momap -i momap_evc.inp

# Step 2: Spectrum (copy ref params)
cp /opt/MOMAP-2024A/tests/azulene/kr/momap.inp momap_spec.inp
momap -i momap_spec.inp

TADF Workflow Integration

For TADF molecules, the MOMAP pipeline is:

Gaussian S0 opt+freq  →  s0.log + s0.fchk
Gaussian T1 opt+freq  →  t1.log + t1.fchk
Gaussian S1 TDDFT     →  s1.log + s1.fchk (vertical + adiabatic)
       ↓
   EVC (S0 vs S1)     →  evc_s1.cart.dat
   EVC (S1 vs T1)     →  evc_t1.cart.dat
       ↓
   spec_tvcf (S1→S0)  →  fluorescence spectrum
   ISC (S1→T1)        →  k_ISC rate
       ↓
   Quantum yield: Φ = k_r / (k_r + k_IC + k_ISC)

Troubleshooting

`mpiexec: Error: unknown option "-machinefile"`

MOMAP was compiled with OpenMPI 1.x, system has 3.x.
Fix: Copy + patch momap script:

cp $MOMAP_BIN/momap momap_patched
sed -i 's/-machinefile/--hostfile/g' momap_patched
echo "localhost slots=4" > nodefile
python momap_patched -i momap.inp

`Can not find Gaussian fchk file!`

MOMAP needs both .log and .fchk files in the same directory.

formchk job.chk job.fchk

spec_tvcf killed (OOM)

Use MPI on a compute node with more memory:

#SBATCH --mem=64G
mpirun -np 4 momap -i momap.inp

Reference files

All test examples with pre-computed Gaussian logs:

/opt/MOMAP-2024A/tests/azulene/gaussian/ref/ — azulene S0/S1
/opt/MOMAP-2024A/tests/porphine/gaussian_g16/ — porphine
/opt/MOMAP-2024A/tests/Irppy3/ — Ir(ppy)₃

Citations

Y. Niu et al., Molecular Physics, 2018, doi: 10.1080/00268976.2017.1402966
Q. Peng et al., J. Am. Chem. Soc., 2007, 129, 9333-9339
Z. Shuai, Q. Peng, Phys. Rep., 2014, 537, 123
Z. Shuai, Q. Peng, Nat. Sci. Rev., 2017, 4, 224

Official: http://www.momap.cn

Toolkit (momap/tools/)

Four Python CLI tools for automated MOMAP workflows:

momap-extract — Gaussian → MOMAP params

python3 tools/extract.py --s0 mol-s0.log --s1 mol-s1.log [--t1 mol-t1.log]
# Output: spec_tvcf input + JSON params (Ead, EDMA, EDME)
# Auto-handles TDDFT: Ead = SCF_S1 + E_exc_adiabatic - SCF_S0

momap-run — One-command MOMAP wrapper

python3 tools/runner.py momap.inp [--slurm] [--nprocs 4]
# Auto: MPI --hostfile patch, formchk (.chk→.fchk), Slurm submit

momap-tadf — Full TADF pipeline

python3 tools/tadf.py mol_id --s0 s0.log --s1 s1.log --t1 t1.log
# Runs: EVC(S1→S0) → spec_tvcf → ISC(S1→T1) → summary
# Output: spectrum, peak λ, blue window check, ΔE_ST

momap-plot — Spectrum visualization

python3 tools/plot.py spec.tvcf.spec.dat -D --blue 450 490
# Pillow fallback if no matplotlib. -D = save to Desktop.
# Prints peak analysis with blue window highlighting.

momap-oled — OLED extended modules (v3)

python3 tools/oled.py isc  --ead 0.094 --hso 116.9          # isc_tvcf → k_ISC
python3 tools/oled.py ic   --ead 0.094 --nac evc.cart.nac   # ic_tvcf → k_IC
python3 tools/oled.py pysoc --com mol.com                    # PySOC → Hso values
python3 tools/oled.py sums --ead 0.094 --dipole-abs 0.09 --dipole-emi 0.44  # Φ, all rates
python3 tools/oled.py transport --cif crystal.cif            # μ_h, μ_e
# Each generates a ready-to-run MOMAP input file.

MOMAP Skill (v2 — 2024A Verified)

Resources

Install

MOMAP Skill (v2 — 2024A Verified)

Server Setup

Real Input Format (MOMAP 2024A)

Step 1: Electron-Vibration Coupling (EVC)

Step 2: Spectrum (spec_tvcf)

Step 3: ISC Rate (isc_tvcf)

Step 4: Internal Conversion (ic_tvcf)

Step 5: Spin-Orbit Coupling (PySOC)

Step 6: Full Rate Summary (spec_sums)

Step 7: Charge Transport (transport)

OLED TADF Design — Complete Workflow

Extracting Parameters from Gaussian Output

Ead (adiabatic excitation energy)

EDMA (absorption transition dipole moment)

EDME (emission transition dipole moment)

Example: Azulene (bundled test)

TADF Workflow Integration

Troubleshooting

mpiexec: Error: unknown option "-machinefile"

Can not find Gaussian fchk file!

spec_tvcf killed (OOM)

Reference files

Citations

Toolkit (momap/tools/)

momap-extract — Gaussian → MOMAP params

momap-run — One-command MOMAP wrapper

momap-tadf — Full TADF pipeline

momap-plot — Spectrum visualization

momap-oled — OLED extended modules (v3)

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Install

Recommended Skills

`mpiexec: Error: unknown option "-machinefile"`

`Can not find Gaussian fchk file!`