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--- exercises:2015_pitt:aimd [2015/03/03 11:58] – vondele
+++ exercises:2015_pitt:aimd [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 6: / Line 6: @@
 The second goal to understand the produced .ener file and do some basic analysis of the trajectory with VMD.
-====== AIMD of water ======
+====== AIMD of bulk liquid water ======
 <note>For the sake of running this exercise quickly, we'll use the DZVP-GTH basis found in the HFX_BASIS file. This basis is smaller than what can be recommended for a subtle substance such as liquid water, rather use TZV2P-GTH, TZV2P-MOLOPT-GTH, or cc-TZV2P or better basis sets for production runs.</note>
@@ Line 174: / Line 174: @@
 How many neighbors does a given water molecule have on average (3, 3-4, 4, 4-5, 5)?
-=== IR spectrum ===
+==== IR spectrum ====
 Based on the time evolution of the dipole of the system, the IR spectral density can be estimated. To estimate the dipole from AIMD, wannier centers need to be computed. This is out of scope of the current tutorial (TODO: find link). We employ a simple approximation, namely classical point charges for the water molecules. In this context the approximation is reasonable.
@@ Line 193: / Line 193: @@
 <note> Lower frequencies need longer trajectories for reasonable estimates, at the very least 10 times the period of the signal </note>
+====== AIMD of simle ions in water solution ======
 ===== 4th task: simple ions in solution =====
@@ Line 201: / Line 202: @@
 The easiest way to do so is to replace one or more water molecules (depending on the size of the ion) by the ion in question. Obviously, the configuration produced in this way is far from equilibrium, and must be run for a while before it is representative.
-Entertaining is to turn one H2O in H+, do you see Eigen and Zundel states and [[wp>Grotthuss_mechanism |the Grotthuss mechanism]] ?
+Entertaining is to turn one H2O into H+, do you see Eigen and Zundel states and [[wp>Grotthuss_mechanism |the Grotthuss mechanism]] ?
 ====== Required files ======
@@ Line 399: / Line 400: @@
   H        -4.1388543582       -6.3621998573        2.1513804320
   H        -4.3955669691       -5.3216936959        1.0405948547
+</code>
+The following file should be the result of your edits to ''mode1.inp'' and your final ''water.inp''. Only use this if you're stuck following the instructions.
+<code - water_cheating.inp>
+&GLOBAL
+  ! the project name is made part of most output files... useful to keep order
+  PROJECT WATER
+  ! various runtypes (energy, geo_opt, etc.) available.
+  RUN_TYPE MD
+  ! limit the runs to 5min
+  WALLTIME 1800
+  ! reduce the amount of IO
+  IOLEVEL  LOW
+&END GLOBAL
+&FORCE_EVAL
+  ! the electronic structure part of CP2K is named Quickstep
+  METHOD Quickstep
+  &DFT
+    ! basis sets and pseudopotential files can be found in cp2k/data
+    BASIS_SET_FILE_NAME HFX_BASIS
+    POTENTIAL_FILE_NAME GTH_POTENTIALS
+    ! Charge and multiplicity
+    CHARGE 0
+    MULTIPLICITY 1
+    &MGRID
+       ! PW cutoff ... depends on the element (basis) too small cutoffs lead to the eggbox effect.
+       ! certain calculations (e.g. geometry optimization, vibrational frequencies,
+       ! NPT and cell optimizations, need higher cutoffs)
+       CUTOFF [Ry] 400
+    &END
+    &QS
+       ! use the GPW method (i.e. pseudopotential based calculations with the Gaussian and Plane Waves scheme).
+       METHOD GPW
+       ! default threshold for numerics ~ roughly numerical accuracy of the total energy per electron,
+       ! sets reasonable values for all other thresholds.
+       EPS_DEFAULT 1.0E-10
+       ! used for MD, the method used to generate the initial guess.
+       EXTRAPOLATION ASPC
+    &END
+    &POISSON
+       PERIODIC XYZ ! the default, gas phase systems should have 'NONE' and a wavelet solver
+    &END
+    &PRINT
+       ! at the end of the SCF procedure generate cube files of the density
+       &E_DENSITY_CUBE OFF
+       &END E_DENSITY_CUBE
+       ! compute eigenvalues and homo-lumo gap each 10nd MD step
+       &MO_CUBES
+          NLUMO 4
+          NHOMO 4
+          WRITE_CUBE .FALSE.
+          &EACH
+            MD 10
+          &END
+       &END
+    &END
+    ! use the OT METHOD for robust and efficient SCF, suitable for all non-metallic systems.
+    &SCF
+      SCF_GUESS ATOMIC ! can be used to RESTART an interrupted calculation
+      MAX_SCF 30
+      EPS_SCF 1.0E-6 ! accuracy of the SCF procedure typically 1.0E-6 - 1.0E-7
+      &OT
+        ! an accurate preconditioner suitable also for larger systems
+        PRECONDITIONER FULL_SINGLE_INVERSE
+        ! the most robust choice (DIIS might sometimes be faster, but not as stable).
+        MINIMIZER DIIS
+      &END OT
+      &OUTER_SCF ! repeat the inner SCF cycle 10 times
+        MAX_SCF 10
+        EPS_SCF 1.0E-6 ! must match the above
+      &END
+      ! do not store the wfn during MD
+      &PRINT
+        &RESTART OFF
+        &END
+      &END
+    &END SCF
+    ! specify the exchange and correlation treatment
+    &XC
+      ! use a PBE functional
+      &XC_FUNCTIONAL
+         &PBE
+         &END
+      &END XC_FUNCTIONAL
+      ! adding Grimme's D3 correction (by default without C9 terms)
+      &VDW_POTENTIAL
+         POTENTIAL_TYPE PAIR_POTENTIAL
+         &PAIR_POTENTIAL
+            PARAMETER_FILE_NAME dftd3.dat
+            TYPE DFTD3
+            REFERENCE_FUNCTIONAL PBE
+            R_CUTOFF [angstrom] 16
+         &END
+      &END VDW_POTENTIAL
+    &END XC
+  &END DFT
+  ! description of the system
+  &SUBSYS
+    &CELL
+      ! unit cells that are orthorhombic are more efficient with CP2K
+      ABC [angstrom] 12.42 12.42 12.42
+    &END CELL
+    ! atom coordinates can be in the &COORD section,
+    ! or provided as an external file.
+    &TOPOLOGY
+      COORD_FILE_NAME water.xyz
+      COORD_FILE_FORMAT XYZ
+    &END
+    ! MOLOPT basis sets are fairly costly,
+    ! but in the 'DZVP-MOLOPT-SR-GTH' available for all elements
+    ! their contracted nature makes them suitable
+    ! for condensed and gas phase systems alike.
+    &KIND H
+      BASIS_SET DZVP-GTH
+      POTENTIAL GTH-PBE-q1
+    &END KIND
+    &KIND O
+      BASIS_SET DZVP-GTH
+      POTENTIAL GTH-PBE-q6
+    &END KIND
+  &END SUBSYS
+&END FORCE_EVAL
+! how to propagate the system, selection via RUN_TYPE in the &GLOBAL section
+&MOTION
+ &GEO_OPT
+   OPTIMIZER BFGS ! Good choice for 'small' systems (use LBFGS for large systems)
+   MAX_ITER  100
+   MAX_DR    [bohr] 0.003 ! adjust target as needed
+   &BFGS
+   &END
+ &END
+ &MD
+   ENSEMBLE NVT  ! sampling the canonical ensemble, accurate properties might need NVE
+   TEMPERATURE [K] 300
+   TIMESTEP [fs] 0.5
+   STEPS 1000
+   # GLE thermostat as generated at http://epfl-cosmo.github.io/gle4md
+   # GLE provides an effective NVT sampling.
+   &THERMOSTAT
+     REGION MASSIVE
+     TYPE GLE
+     &GLE
+       NDIM 5
+       A_SCALE [ps^-1] 1.00
+       A_LIST    1.859575861256e+2   2.726385349840e-1   1.152610045461e+1  -3.641457826260e+1   2.317337581602e+2
+       A_LIST   -2.780952471206e-1   8.595159180871e-5   7.218904801765e-1  -1.984453934386e-1   4.240925758342e-1
+       A_LIST   -1.482580813121e+1  -7.218904801765e-1   1.359090212128e+0   5.149889628035e+0  -9.994926845099e+0
+       A_LIST   -1.037218912688e+1   1.984453934386e-1  -5.149889628035e+0   2.666191089117e+1   1.150771549531e+1
+       A_LIST    2.180134636042e+2  -4.240925758342e-1   9.994926845099e+0  -1.150771549531e+1   3.095839456559e+2
+     &END GLE
+   &END THERMOSTAT
+ &END
+  &PRINT
+   &TRAJECTORY
+     &EACH
+       MD 1
+     &END EACH
+   &END TRAJECTORY
+   &VELOCITIES OFF
+   &END VELOCITIES
+   &FORCES OFF
+   &END FORCES
+   &RESTART_HISTORY
+     &EACH
+       MD 500
+     &END EACH
+   &END RESTART_HISTORY
+   &RESTART
+     BACKUP_COPIES 3
+     &EACH
+       MD 1
+     &END EACH
+   &END RESTART
+  &END PRINT
+&END
+&EXT_RESTART
+  RESTART_FILE_NAME WATER-1.restart
+&END
 </code>