These commands are used to build up the database. The build commands have the general form:
BuildCommand Parameters Test
where
BuildCommand: Specifies which database element is to be modified
Parameters: The parameters needed, for example the filename of the file to be read in and, in some cases, the reference name.
Test: If true, then the database will not be modified, but the file input file tested. If false, then the database will be modified.
Before running any command which modifies the database, it is suggested that you backup (see below) the database first.
It is also recommended that you use the 'Test' parameter to read in the data file first before modifying the database:
true: This will just read in the file and print out to the terminal the file information as interpreted. It is suggested that this information be checked before modifying the current database. Error can occur on reading and hopefully you can decipher where the problem lies.
false: The file will be read in and the database modified.
These are the parameters used in the commands:
'ReferenceName' is the name of the source type of this data (for example "Standard")
'FileName: The absolute location of the file to read in.
'Type': A catagory (for example, of substructures)
'Test': Just read in the appropriate file, without storing in the database.
Commands for entering thermodynamic information through files
Benson Filename ReferenceName Test: Reads in Benson thermodynamic information (ex Table A.1 and Table 2.14 in Benson's book)
Molecules Filename ReferenceName Test: This parses a file of thermodynamics for molecules, in Benson format of standard enthalpy, standard entropy and heat capacities, for molecules (ex. Tables A.7 to A.11 in Benson)
SubstructureThermo Filename Type ReferenceName Test: This reads in the thermodynamics, , in Benson format of standard enthalpy, standard entropy and heat capacities, for substructures. This is used for reading in corrections based on substructures. (such as ring compound estimates in Table A.1 in Benson or even the HBI groups of the THERM method).
Commands to read in structural information:
Substructures Filename ReferenceName Test: Each line specifies a structure, the name of the structure and the type of structure. This is used, for example, to define the symmetry elements (in the symmetry element definition, only the structure name is specified).
MetaAtoms Filename Test: This defines a set of meta-atoms, including structure, the name of the structure, the name of the meta-atom and the type of meta-atom. Two examples are defining Benson atoms (such as single, double or triple bonded atoms or groups such as CO) and linear atom groups.
Commands to read in correction information:
SymmetryDefinition Filename Test: Reads in symmetry information. The symmetry information is defined relative to a specific molecular structure in the database.
Vibrational Filename ReferenceName Test: Reads in vibrational frequency and symmetry for a substructure .
DisassociationEnergy Filename ReferenceName Test: Read disassociation values for radicals.
Delete Database ReferenceName: Delete all reference name elements from database
BondLengths Filename ReferenceName Test: Read in bond lengths
Table Filename: Build a calculation matrix for linear regression
If you are modifying the database, it is highly recommended that you backup the mySQL data so you can recover the previous database. Below you will find instructions on how to do this with mysql line commands. You can also use tools such as the mySQLWorkbench to accomplish this task.
Assuming that the database is named thermodynamics, the mysqldump command can be used to make a copy of the current database:
mysqldump -u root -pPassword thermodynamics > thermodynamics20210101.backup.sql
Substitute your password, database name and file name (it is suggested that the date or version is included) in the above command.
If you need to recover the database, assuming that the database is called thermodynamics and the file is called thermodynamics.backup.sql
mysql -u root -p thermodynamics < thermodynamics20210101.backup.sql
Again, substitute your password, database name and file name in the above command. In this command, you will be asked for the root password.