Frequently Asked Questions

How to restart an interrupted calculation?

BDF supports restarting several common types of calculations from a checkpoint, including:

SCF Single Point Energy: Use the guess keyword to read the molecular orbitals from the last SCF iteration of the interrupted job as the initial guess. Specifically, set the initial guess to readmo in the $scf module and rerun the input file.

$scf
...
guess
 readmo
$end

TDDFT Single Point Energy: When a TDDFT job is interrupted and idiag ≠ 2, you can read the TDDFT excitation vectors from the last iteration of the interrupted job (Davidson iteration when idiag=1, iVI iteration when idiag=3) as the initial guess. Note: when idiag=3, restart is only possible for calculations with C(1) symmetry.

To restart a TDDFT job: - Use the guess readmo keyword in the $scf module to read the converged SCF wavefunction from the interrupted job. - Use the iguess keyword in the $tddft module to specify reading the TDDFT excitation vectors from the interrupted job. For example, suppose the original input file contained:
```
$scf
...
$end

$tddft
...
iguess
 21
$end
```
Here, iguess=21 (2 indicates tight-binding initial guess; 1 writes excitation vectors at each iteration to files: .dvdsonvec* for idiag=1 or .tdx for idiag=3). If this job is interrupted, modify the input file as follows for restart:
```
$scf
...
guess
 readmo
$end

$tddft
...
iguess
 11 # or 10 if sure the job won't be interrupted again
$end
```
guess readmo reads the previous SCF orbitals to avoid redoing SCF. iguess=11 (1 reads excitation vectors from files). See the tddft section for details on iguess options.

Important Notes: - (1) Due to the nature of Davidson/iVI methods, restarting saves fewer TDDFT iterations compared to SCF. Restarting may not save iterations unless the previous TDDFT run was near convergence. - (2) TDDFT does not save intermediate excitation vectors by default. Specify iguess=1, 11, or 21 to enable saving. Not enabling this in the original run prevents restart. Saving vectors increases disk I/O; users must weigh this trade-off.
Geometry Optimization: Add the restart keyword in the $compass module. See the compass section.
Numerical Frequency Calculation: Add the restarthess keyword in the $bdfopt module. See the bdfopt section.

How to cite BDF?

When using BDF, cite the original BDF papers [1, 92, 93, 94]. Additionally, cite the relevant papers for specific features used; see the Quote Notes section.

TDDFT: Imaginary/Complex Excitation Energies

If the ground state wavefunction is unstable or the SCF converged to a non-ground state, TDDFT may produce imaginary excitation energies, rarely even complex ones. These lack physical meaning. - With the Davidson method (idiag=1), a Warning: Imaginary Excitation Energy! is issued, and the modulus of all imaginary/complex energies is printed upon convergence. - With the iVI method (idiag=3), an Error in ETDVSI: ABBA mat is not positive! Suggest to use nH-iVI. warning is issued. Subsequent calculations only solve for real excitation energies (thus, convergence to real energies does not guarantee the absence of imaginary/complex states. Solution: Re-optimize the ground state to find a stable solution or use TDA for excitation energies.

TDDFT J/K Operator Memory & Efficiency

If solving for many roots, default TDDFT memory may be insufficient, reducing efficiency. The TDDFT keyword MEMJKOP sets the maximum memory for J/K operator calculation. Example output when requesting 4 roots:

Maximum memory to calculate JK operator:        1024.000 M
Allow to calculate    2 roots at one pass for RPA ...
Allow to calculate    4 roots at one pass for TDA ...

This indicates 1024 MB (Megabytes) is available for J/K operators. For RPA (full TDDFT), 2 roots can be processed per integral evaluation pass; for TDA, 4 roots. For TDA, all roots are processed in one pass. For RPA, two passes are needed (reduced efficiency). Setting MEMJKOP to 2048MB allows processing all 4 roots in one pass (RPA). Note: Physical memory usage ≈ 2048MB * OMP_NUM_THREADS.

Segmentation Fault & Stack Memory Limits

Most segmentation faults in BDF are caused by insufficient stack memory. On Linux, use the ulimit command to set stack size.

Check current limits:

ulimit -a

Example output:

core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
...
stack size              (kbytes, -s) 4096
...

Here, stack size ... 4096 indicates a 4096 KB (4 MB) limit. Set to unlimited:

ulimit -s unlimited

Note: Stack size has a hard limit set by the system. If ulimit -s unlimited fails:

bash: ulimit: stack size: cannot modify limit: Operation not permitted

Contact your system administrator to increase the hard limit or use root privileges.

Sometimes, segmentation faults can also stem from insufficient OpenMP stack memory. Setting ulimit alone may not suffice; environment variables like OMP_STACKSIZE and KMP_STACKSIZE may also need adjustment. See section OpenMP Stack Memory Size.

OpenMP Parallel Computing

BDF supports OpenMP parallelism. Set the number of threads in your run script:

export OMP_NUM_THREADS=8

This allows up to 8 OpenMP threads.

OpenMP Stack Memory Size

Intel compilers (and others) place dynamic memory from parallel regions on the stack for efficiency. Users must set the per-thread stack size in the run script:

export OMP_STACKSIZE=2048M

This sets 2048MB per thread. Total stack memory usage = OMP_STACKSIZE * OMP_NUM_THREADS.

Important

OMP_STACKSIZE is a generic variable. Priority for OpenMP stack size environment variables is:

KMP_STACKSIZE (Intel OpenMP) > GOMP_STACKSIZE (GNU OpenMP) > OMP_STACKSIZE

Higher-priority variables set in the script will override OMP_STACKSIZE.

Intel Fortran Compiler 2018

The Intel 2018 Fortran compiler has known bugs. Avoid using it to compile BDF.

SCF Non-Convergence

See section Handling SCF Convergence Problems in the SCFTech chapter.

SCF Energy Significantly Lower Than Expected (>1 Hartree) or Displayed as Asterisks

Usually caused by linear dependence in the basis set. See the discussion on basis set linear dependence under Handling SCF Convergence Problems in the SCFTech chapter. Note: While the chapter focuses on SCF non-convergence, the solutions also apply to cases where linear dependence causes incorrect SCF energies without preventing convergence.

How to Use Custom Basis Sets

See section Custom Basis Set Files in Gaussian-Basis-Set.

Program Exits Without Performing Any Calculation

If the program outputs “Warning!!! The following input line is skipped. You may need to check the input file!” and exits without calculation:

First check the input file for obvious errors, especially for concise input, the first line must start with ‘’#!’’. If not, check to see if there are extra spaces in front of certain lines, especially the first line of the input file. When using concise input, there must be no spaces in front of the ‘’#!’’ in the first line, if the user is copying the input file from elsewhere, it may copy some more spaces due to typography problems, and these spaces must be manually deleted.