Documentation
Files
Filenames used by GronOR are derived from user-defined identifiers root and calc, such that all integral
and wavefunction files generated using the OpenMolcas program only use the root identifier in the
filename, and individual GronOR calculations use root_calc filenames. This allows different GronOR
calculations differentiated by calc to be carried out with the same OpenMolcas generated files.
In the following table boldface typed files are required in any GronOR calculation.
File Name
Description
Origin
root.one
One-electron integral file
OpenMolcas & rdtraint
root_nnn.two
Two-electron file(s)
OpenMolcas & rdtraint
root.sys
Molecular definition file
OpenMolcas & rdtraint
root_nnn.vec
MO vector files(s)
OpenMolcas
root_nnn.det
Determinants file(s)
OpenMolcas
root_calc.inp
Input file for GronOR
Editor
root_calc.out
Output file
GronOR
root_calc.arx
Archive file
GronOR
root_calc.cpr
Checkpoint Restart file
GronOR
root_calc.cml
CML-formatted output file
GronOR
root_calc.day
Dayfile
GronOR
root_calc.pro
Progress file
GronOR
root_calc.rnk
Rank assignment file
GronOR
root_calc.tst
Test file for automated testing
GronOR
root_calc.xyz
XYZ-formatted coordinates
GronOR
root.log
Log file
GronOR
gronor_nnn.dbg
Debug file(s)
GronOR
The type of file is identified by its extension, as follows:
inp: Input for GronOR.
out: Output from GronOR.
one: One electron integrals provided by OpenMolcas.
two: Two-electron integrals provided by OpenMolcas. These intrgrals can be provided over multiple
files as a way to reduce repeat file transfers over unreliable connections
sym: Symmetry information provided by OpenMolcas.
xyz: XYZ-formatted coordinates
vec: Vector files provided by OpenMolcas
det: Determinant files provided by OpenMolcas
arx: Archive file that can be read by the Java tool
cml: CML-formatted file for uploading to ioChem-BD.
cpr: Checkpoint Restart file. If this file is present it indicates that a previous run aborted on an
error or time limit. Restarting the same job will cause this file to be read and the calculation will
continue from the last result written to the cpr file. If a calculation finishes correctly, there will
not be a cpr file.
day: The day file will have periodic entries added as a calculation proceeds. This file can be
monitored to see if a job continues to make progress.
log: Summary file with results from all jobs run in the current directory that used the same root
files.
rnk: The rank file will contain information about the ranks used and their assignments and can be
used to determine if the job parameters were correctly specified.
tst: Test data for automated testing used by developers.
pro: A progress file used by developers.
dbg: Debug files, generated one per rank, used by developers.
Input (Key-Value pair combinations on file root_calc.inp)
Keyword
Description
Format
Default
Required
MEBFs
Number of many electron basis functions,
integer
Yes
followed by integer fragment identifiers
one line for each fragment
Size
Number of ranks per worker group
integer
1
No
Spin
Spin multiplicity
integer
1
No
Task
Number of ME contributions per task
integer
32 32
No
for accelerated and non-accelerated ranks
Batch
Number of ME contributions calculated in a
integer
1 32
No
single pass through integrals
for accelerated and non-accelerated ranks
Threshold
Threshold expansion coefficients
real
1.0d-5
No
Acceleration
Number of accelerated ranks per node
integer
1
No
Threads
Number OpenMP threads, non-accelerated ranks
integer
1
No
Solver
Library solver options
integer
1 0 1 0
No
Acc CUSOLVER SVD 0: no, 1: QR, 2: Jacobi
Acc CUSOLVER EVD 0: no, 1: QR, 2: Jacobi
Non-acc SVD 0: no, 1: MKL or other
Non-acc EVD 0: no, 1: MKL or other
Tolerance
Tolerance CUSOLVER Jacobi solvers
real
1.0e-07
No
Values for SVD and EVD
Sweep
Number Jacobi sweeps
integer
15 15
No
Values for SVD and EVD
Ecorr
Dynamic correlation energy correction per state
real
0.0d0
No
GNWeights
Gallup-Norbeck weights
integer
0
No
0: off 1: on
Print
Print option
string
medium
No
low:
minimal input data and final resuls
medium: default input data and final results
high:
debug:
Dayfile
Percent complete written to separate file
integer
10
No
MEBFs: This keyword is the only required keyword. It specifies the number of many-electron basis
functions to be constructed from the state wavefunctions specified on the following cards. Each card is
a list of states for a single molecule or fragment. The use should give as many of these cards as the
number of molecules or fragments to be included. GronOR will automatically determine the number
of molecules or fragments from the number of cards provided.
Spin: The keyword specifies the total spin state of the combined many-electron basis functions. The
default is the singlet state. Therefore, Spin only needs to be specified for higher than singlet spin states.
Size: In cases where the memory require to store the two-electron integrals exceeds the available memory
on the node, or on an accelerator, the integrals can be divided over multiple ranks such that multiple nodes
or multiple accelerators are used for a single copy of the two-electron integrals. The number of ranks to be
used in this way is specified by the Size input variable.
Acceleration: By default all ranks with access to an accelerator will be assigned to use the accelerator. In
cases where the users wants to use accelerated and non-accelerated ranks on a node with a device, the
keyword Accelerator specifies the number of ranks on node that will use the accelerator leaving the
remaining ranks on that node to use the CPU only.
Threads: If GronOR was compiled with the -DOPENMP=ON flag, the keyword Threads can be used to
specify the number of OpenMP threads that a rank will use. By default, non-accelerated ranks, even when
compiled with for OpenMP threading, will use a single thread. When Threads is not specified, but the
environment variable NUM_OMP_THREADS is set, GronOR will use the value specified by the
enviroment variable. If Threads is specified, it will override any value of the NUM_OMP_THREADS
enviroment variable.
Solvers: GronOR uses the most efficient available solvers depending on the chemical system size. In
practice it should not be necessary to specify Solvers explicitly.
Task: This is the number of matrix element contributions that will be calculated in a single task from the
master to worker ranks. Increasing Task will result in fewer communication operations. The default value
of 32 appears optimal for most siutations.
Batch: This is the number of matrix element contributions calculated with a singke sweep through the
two-electron integrals. In practice, this option is only resulting in reduced wall clock time on CPU-only
ranks. The valkue of Batch can not exceed the value of Task. The default of 32 in GronOR for
non-accelerated ranks appears optimal in most cases.
Input for developers (Key-Value pair combinations on root_calc.inp)
Keyword
Description
Format
Default
Required
Timings
Wall clock timings analysis
integer
0
No
Progress
Communication events to progress file
integer
0
No
0:
no progress file
1:
matrix elements only
2:
all communication events
3:
as 1 but accumulated and file saved
4:
as 2 but accumulated and file saved
Test
Flag to write test file
integer
0
No
Debug
Debug output level (one file per rank)
integer
0
No
MPIbuffer
Size two-electron MPI buffer
integer
168435456
No
Expert
Option for expert options
integer
0
No
Development
Use of development code
integer
0
No