howto:geometry_optimisation
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision | ||
geometry_optimisation [2014/01/28 08:31] – ibethune | howto:geometry_optimisation [2014/02/09 15:14] – oschuett | ||
---|---|---|---|
Line 1: | Line 1: | ||
- | ====== | + | ====== |
+ | ===== Introduction ===== | ||
This tutorial is designed to illustrate how to relax the structure | This tutorial is designed to illustrate how to relax the structure | ||
- | of a system (without changing the cell dimensions) using '' | + | of a system (without changing the cell dimensions) using '' |
use the relaxation of a water (H\(_2\)O) molecule as an example. | use the relaxation of a water (H\(_2\)O) molecule as an example. | ||
- | The example files are contained in {{: | + | The example files are contained in {{: |
2.4. | 2.4. | ||
Line 16: | Line 17: | ||
tutorial [[converging_cutoff|Converging the CUTOFF and REL_CUTOFF]]). | tutorial [[converging_cutoff|Converging the CUTOFF and REL_CUTOFF]]). | ||
- | ====== Input Files ====== | ||
+ | ===== Input Files ===== | ||
The input file for a geometry calculation is shown below: | The input file for a geometry calculation is shown below: | ||
Line 101: | Line 102: | ||
&END CONSTRAINT | &END CONSTRAINT | ||
&END MOTION | &END MOTION | ||
- | </ | + | </ |
- | The reader should already be familiar with the [[http:// | + | The reader should already be familiar with the [[http:// |
- | [[http:// | + | [[http:// |
- | must set [[http:// | + | must set [[http:// |
<code cp2k> | <code cp2k> | ||
RUN_TYPE GEO_OPT | RUN_TYPE GEO_OPT | ||
- | </ | + | </ |
In this example, we note that we have chosen diagonalisation of the | In this example, we note that we have chosen diagonalisation of the | ||
Line 117: | Line 118: | ||
The important section for geometry optimisation settings are | The important section for geometry optimisation settings are | ||
- | contained in subsection [[http:// | + | contained in subsection [[http:// |
- | '' | + | '' |
dimensions do not change. Calculations which allows the relaxation | dimensions do not change. Calculations which allows the relaxation | ||
of the cell are covered in a separate tutorial. | of the cell are covered in a separate tutorial. | ||
Line 136: | Line 137: | ||
&END CG | &END CG | ||
&END GEO_OPT | &END GEO_OPT | ||
- | </ | + | </ |
- | The [[http:// | + | The [[http:// |
- | finding the local minima ('' | + | finding the local minima ('' |
- | point transition state ('' | + | point transition state ('' |
- | [[http:// | + | [[http:// |
- | optimised geometry is reached. '' | + | optimised geometry is reached. '' |
the tolerance on the maximum and root-mean-square of atomic | the tolerance on the maximum and root-mean-square of atomic | ||
displacements from the previous geometry optimisation iteration; | displacements from the previous geometry optimisation iteration; | ||
- | '' | + | '' |
the maximum and root-mean-square of atomic forces. The geometry is | the maximum and root-mean-square of atomic forces. The geometry is | ||
considered to be optimised //only when all four criteria are | considered to be optimised //only when all four criteria are | ||
- | satisfied// | + | satisfied// |
- | geometry optimisation iterations. [[http:// | + | geometry optimisation iterations. [[http:// |
finding the stationary points; in this example we have chosen the | finding the stationary points; in this example we have chosen the | ||
- | conjugate gradients ('' | + | conjugate gradients ('' |
- | The [[http:// | + | The [[http:// |
algorithm. In this case, we have configured it so that no steepest | algorithm. In this case, we have configured it so that no steepest | ||
descent steps are to be performed before the start of the conjugate | descent steps are to be performed before the start of the conjugate | ||
Line 167: | Line 168: | ||
&END FIXED_ATOMS | &END FIXED_ATOMS | ||
&END CONSTRAINT | &END CONSTRAINT | ||
- | </ | + | </ |
- | We can add constraints to atomic movements by using the [[http:// | + | We can add constraints to atomic movements by using the [[http:// |
- | subsection in '' | + | subsection in '' |
- | particular atoms using the [[http:// | + | particular atoms using the [[http:// |
- | [[http:// | + | [[http:// |
be fixed, and in this case, the atoms will be completely pinned in | be fixed, and in this case, the atoms will be completely pinned in | ||
- | all directions ('' | + | all directions ('' |
- | given by the [[http:// | + | given by the [[http:// |
<code cp2k> | <code cp2k> | ||
LIST 1 2 3 ... N | LIST 1 2 3 ... N | ||
- | </ | + | </ |
- | The numbers to the right of '' | + | The numbers to the right of '' |
and correspond to the order (from top to bottom) of the atoms given | and correspond to the order (from top to bottom) of the atoms given | ||
- | in the [[http:// | + | in the [[http:// |
example, we have fixed the oxygen atom during geometry optimisation, | example, we have fixed the oxygen atom during geometry optimisation, | ||
so that the water molecule will not move around while its structure | so that the water molecule will not move around while its structure | ||
is being relaxed. | is being relaxed. | ||
- | ====== Results ====== | ||
- | The example is run using the serial version of the '' | + | |
+ | ===== Results ===== | ||
+ | The example is run using the serial version of the '' | ||
< | < | ||
cp2k.sopt -o H2O.out H2O.inp & | cp2k.sopt -o H2O.out H2O.inp & | ||
- | </ | + | </ |
After the job has finished, you should obtain the following files: | After the job has finished, you should obtain the following files: | ||
- | * '' | + | * '' |
- | * '' | + | * '' |
- | * '' | + | * '' |
- | * '' | + | * '' |
- | * '' | + | * '' |
- | * '' | + | * '' |
- | Again, the file '' | + | Again, the file '' |
- | job. '' | + | job. '' |
- | each geometry optimisation step in the '' | + | each geometry optimisation step in the '' |
set of atomic coordinates corresponds to the relaxed | set of atomic coordinates corresponds to the relaxed | ||
- | structure. '' | + | structure. '' |
- | '' | + | '' |
molecule. Should the job die for some reason, you can continue the | molecule. Should the job die for some reason, you can continue the | ||
job using the latest atomic coordinates by using command: | job using the latest atomic coordinates by using command: | ||
Line 215: | Line 217: | ||
< | < | ||
cp2k.sopt -o H2O.out H2O-1.restart & | cp2k.sopt -o H2O.out H2O-1.restart & | ||
- | </ | + | </ |
- | You can of course also use '' | + | You can of course also use '' |
an input for further calculations using the relaxed atomic | an input for further calculations using the relaxed atomic | ||
structures. | structures. | ||
- | The files '' | + | The files '' |
atomic coordinates obtained from the previous 1, 2 and 3 geometry | atomic coordinates obtained from the previous 1, 2 and 3 geometry | ||
- | optimisation iterations. '' | + | optimisation iterations. '' |
- | '' | + | '' |
- | In the main output file '' | + | In the main output file '' |
optimisation step, we will have the following information: | optimisation step, we will have the following information: | ||
Line 251: | Line 253: | ||
Conv. for gradients | Conv. for gradients | ||
--------------------------------------------------- | --------------------------------------------------- | ||
- | </ | + | </ |
The above output segment states that at the end of geometry | The above output segment states that at the end of geometry | ||
Line 257: | Line 259: | ||
-17.1643447508 (Ha) and none of the criteria for optimised geometry | -17.1643447508 (Ha) and none of the criteria for optimised geometry | ||
has been reached. The iteration therefore will carry on, until all | has been reached. The iteration therefore will carry on, until all | ||
- | criteria becomes "'' | + | criteria becomes "'' |
At the end of geometry optimisation, | At the end of geometry optimisation, | ||
Line 284: | Line 286: | ||
Conv. in RMS gradients | Conv. in RMS gradients | ||
--------------------------------------------------- | --------------------------------------------------- | ||
- | </ | + | </ |
which clearly shows all criteria have been satisfied. | which clearly shows all criteria have been satisfied. | ||
Line 342: | Line 344: | ||
ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): | ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): | ||
- | </ | + | </ |
howto/geometry_optimisation.txt · Last modified: 2024/01/15 09:23 by oschuett