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updated doc pages and README files

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This commit is contained in:
Steve Plimpton
2023-02-24 13:32:58 -07:00
parent de98704e1e
commit 37d6014f40
7 changed files with 168 additions and 128 deletions
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27
examples/QUANTUM/LATTE/README
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@ -1,14 +1,25 @@
# Test runs with coupling of LAMMPS and LATTE
Step 1: build LAMMPS
Step 2: download/build MDI code coupling package
Step 3: download/build LATTE
Step 4: perform test runs in any of 3 modes
Step 0: What LATTE currently supports
Step 1: Build LAMMPS
Step 2: Download/build MDI code coupling package
Step 3: Download/build LATTE
Step 4: Perform test runs in any of 3 modes
---------------------------------
---------------------------------
Step 1: build LAMMPS
Step 0: What LATTE currently supports
LATTE can be used with fix mdi/qm to perform QM calculations of an
entire system, but not with fix mdi/qmmm to perform QMMM simulations.
LATTE can calculate a QM energy and virial as well as QM forces on
each atom.
---------------------------------
---------------------------------
Step 1: Build LAMMPS
The MDI and molecule packags are needed. Copy the final LAMMPS
executable into the examples/QUANTUM/LATTE directory.
@ -33,7 +44,7 @@ CMake:
---------------------------------
---------------------------------
Step 2: download/build MDI code coupling package
Step 2: Download/build MDI code coupling package
(a) clone the MDI Git repo
@ -71,7 +82,7 @@ will need:
---------------------------------
---------------------------------
Step 3: download/build LATTE
Step 3: Download/build LATTE
(a) clone the skimLATTE repo
@ -101,7 +112,7 @@ For (t)csh:
---------------------------------
---------------------------------
Step 4: perform test runs in any of 3 modes
Step 4: Perform test runs in any of 3 modes
These tests are in lammps/examples/QUANTUM/LATTE

26
examples/QUANTUM/NWChem/README
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@ -1,14 +1,26 @@
# Test runs with coupling of LAMMPS and NWChem PWDFT
Step 0: What NWChem currently supports
Step 1: build LAMMPS
Step 2: download/build MDI code coupling package
Step 3: download/build NWChem PWDFT
Step 4: perform test runs in any of 3 modes
Step 2: Download/build MDI code coupling package
Step 3: Download/build NWChem PWDFT
Step 4: Perform test runs in any of 3 modes
---------------------------------
---------------------------------
Step 1: build LAMMPS
Step 0: What NWChem currently supports
NWChem can be used with fix mdi/qm to perform QM calculations of an
entire system and with fix mdi/qmmm for QMMM simulations. For QMMM it
can use the potential mode of fix mdi/qmmm, but not the direct mode.
NWChem can calculate a QM energy and QM forces on each atom, but it
cannot compute a QM stress tensor.
---------------------------------
---------------------------------
Step 1: Build LAMMPS
The MDI and molecule packags are needed. Copy the final LAMMPS
executable into the examples/QUANTUM/NWChem directory.
@ -33,7 +45,7 @@ CMake:
---------------------------------
---------------------------------
Step 2: download/build MDI code coupling package
Step 2: Download/build MDI code coupling package
(a) clone the MDI Git repo
@ -71,7 +83,7 @@ NWChem will need:
---------------------------------
---------------------------------
Step 3: download/build NWChem PWDFT
Step 3: Download/build NWChem PWDFT
(a) clone the PWDFT Git repo
@ -101,7 +113,7 @@ For (t)csh:
---------------------------------
---------------------------------
Step 4: perform test runs in any of 3 modes
Step 4: Perform test runs in any of 3 modes
These tests are in lammps/examples/QUANTUM/NWChem

2
examples/QUANTUM/NWChem/nwchem_mdi.py
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@ -162,7 +162,7 @@ def mdi_engine(other_options):
mdi.MDI_Register_Command("@DEFAULT","<PE")
mdi.MDI_Register_Command("@DEFAULT","<FORCES")
mdi.MDI_Register_Command("@DEFAULT",">LATTICE_FORCES")
mdi.MDI_Register_Command("@DEFAULT","<STRESS")
#mdi.MDI_Register_Command("@DEFAULT","<STRESS")
mdi.MDI_Register_Command("@DEFAULT","<CHARGES")
# load PWDFT lib and set ctypes signatures for function calls

28
examples/QUANTUM/PySCF/README
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@ -1,14 +1,26 @@
# Test runs with copuling of LAMMPS and PySCF
Step 1: build LAMMPS
Step 2: download/build MDI code coupling package
Step 3: download/build PySCF
Step 4: perform test runs in any of 3 modes
Step 0: What PySCF currently supports
Step 1: Build LAMMPS
Step 2: Download/build MDI code coupling package
Step 3: Download/build PySCF
Step 4: Perform test runs in any of 3 modes
---------------------------------
---------------------------------
Step 1: build LAMMPS
Step 0: What PySCF currently supports
LATTE can be used with fix mdi/qmmm for QMMM simulations, but not with
fix mdi/qm to perform QM calculations of an entire system. For QMMM
it can use the direct mode of fix mdi/qmmm, but not the potential
mode. PySCF can calculate a QM energy and QM forces on each atom, but
it cannot compute a QM stress tensor.
---------------------------------
---------------------------------
Step 1: Build LAMMPS
The MDI, molecule, and kspace packages are needed. Copy the final
LAMMPS executable into the examples/QUANTUM/PySCF directory.
@ -33,7 +45,7 @@ CMake:
---------------------------------
---------------------------------
Step 2: download/build MDI code coupling package
Step 2: Download/build MDI code coupling package
(a) clone the MDI Git repo
@ -63,7 +75,7 @@ For (t)csh:
---------------------------------
---------------------------------
Step 3: download/build PySCF
Step 3: Download/build PySCF
See https://pyscf.org/install.html for install options.
This describes building PySCF from source code.
@ -107,7 +119,7 @@ will need:
---------------------------------
---------------------------------
Step 4: perform test runs in any of 3 modes
Step 4: Perform test runs in any of 3 modes
These tests are in lammps/examples/QUANTUM/PySCF

2
examples/QUANTUM/PySCF/pyscf_mdi.py
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@ -192,7 +192,7 @@ def mdi_engine(other_options):
mdi.MDI_Register_Command("@DEFAULT","<PE")
mdi.MDI_Register_Command("@DEFAULT","<FORCES")
mdi.MDI_Register_Command("@DEFAULT","<LATTICE_FORCES")
mdi.MDI_Register_Command("@DEFAULT","<STRESS")
#mdi.MDI_Register_Command("@DEFAULT","<STRESS")
mdi.MDI_Register_Command("@DEFAULT","<CHARGES")
# one-time operation to establish a connection with the driver