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View Code? Open in Web Editor NEWBenchmarks and examples for Grimme's semiempirical GFNn-xTB
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check omp export OMP_MAX_ACTIVE_LEVELS
export OMP_MAX_ACTIVE_LEVELS=0 creates bad performance, maybe due to bound processors, need to check on clean environment.
OMP_STACKSIZE=1G
OMP_PROC_BIND=true
MKL_NUM_THREADS=10
OMP_MAX_ACTIVE_LEVELS=20
OMP_NUM_THREADS=44
time xtb mol-269.xyz --opt extreme
------------------------------------------------------------------------
* finished run on 2020/03/06 at 07:14:13.300
------------------------------------------------------------------------
total:
* wall-time: 0 d, 0 h, 0 min, 41.888 sec
* cpu-time: 0 d, 0 h, 0 min, 41.854 sec
* ratio c/w: 0.999 speedup
SCF:
* wall-time: 0 d, 0 h, 0 min, 0.230 sec
* cpu-time: 0 d, 0 h, 0 min, 0.230 sec
* ratio c/w: 1.000 speedup
ANC optimizer:
* wall-time: 0 d, 0 h, 0 min, 41.432 sec
* cpu-time: 0 d, 0 h, 0 min, 41.431 sec
* ratio c/w: 1.000 speedup
normal termination of xtb
real 0m41.892s
user 0m41.377s
sys 0m0.481s
export OMP_MAX_ACTIVE_LEVELS=1 creates double the performance
------------------------------------------------------------------------
* finished run on 2020/03/06 at 07:16:25.940
------------------------------------------------------------------------
total:
* wall-time: 0 d, 0 h, 0 min, 19.201 sec
* cpu-time: 0 d, 0 h, 14 min, 3.485 sec
* ratio c/w: 43.930 speedup
SCF:
* wall-time: 0 d, 0 h, 0 min, 0.123 sec
* cpu-time: 0 d, 0 h, 0 min, 5.354 sec
* ratio c/w: 43.596 speedup
ANC optimizer:
* wall-time: 0 d, 0 h, 0 min, 18.958 sec
* cpu-time: 0 d, 0 h, 13 min, 53.968 sec
* ratio c/w: 43.991 speedup
normal termination of xtb
real 0m19.211s
user 13m34.691s
sys 0m28.855s
export OMP_NUM_THREADS=22,44
export OMP_NUM_THREADS=22,1
lower thread count is faster, due to less thermal throttling and higher Mhz clock, despite 96 threads available on CPU. That means in this case a $12,000 Dollar CPU is as fast as a $1000 Dollar CPU.
------------------------------------------------------------------------
* finished run on 2020/03/06 at 07:28:57.110
------------------------------------------------------------------------
total:
* wall-time: 0 d, 0 h, 0 min, 17.418 sec
* cpu-time: 0 d, 0 h, 6 min, 22.387 sec
* ratio c/w: 21.953 speedup
SCF:
* wall-time: 0 d, 0 h, 0 min, 0.107 sec
* cpu-time: 0 d, 0 h, 0 min, 2.338 sec
* ratio c/w: 21.787 speedup
ANC optimizer:
* wall-time: 0 d, 0 h, 0 min, 17.214 sec
* cpu-time: 0 d, 0 h, 6 min, 18.502 sec
* ratio c/w: 21.988 speedup
normal termination of xtb
real 0m17.427s
user 6m10.136s
sys 0m12.384s
LOL: Recommended Customer Price $13012.0 via Intel ARK
~/intel$ lscpu
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
CPU(s): 96
On-line CPU(s) list: 0-95
Thread(s) per core: 2
Core(s) per socket: 24
Socket(s): 2
NUMA node(s): 2
Vendor ID: GenuineIntel
CPU family: 6
Model: 85
Model name: Intel(R) Xeon(R) Platinum 8275CL CPU @ 3.00GHz
Stepping: 7
CPU MHz: 3149.476
BogoMIPS: 6000.00
Hypervisor vendor: KVM
Virtualization type: full
L1d cache: 32K
L1i cache: 32K
L2 cache: 1024K
L3 cache: 36608K
NUMA node0 CPU(s): 0-23,48-71
NUMA node1 CPU(s): 24-47,72-95
Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ss ht syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon rep_good nopl xtopology nonstop_tsc cpuid aperfmperf tsc_known_freq pni pclmulqdq monitor ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm 3dnowprefetch invpcid_single pti fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid mpx avx512f avx512dq rdseed adx smap clflushopt clwb avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves ida arat pku ospke avx512_vnni
Recommended Customer Price: $1089.00 ARK
xtb mol-269.xyz --opt extreme
------------------------------------------------------------------------
* finished run on 2020/03/05 at 23:16:54.321
------------------------------------------------------------------------
total:
* wall-time: 0 d, 0 h, 0 min, 21.252 sec
* cpu-time: 0 d, 0 h, 2 min, 46.937 sec
* ratio c/w: 7.855 speedup
SCF:
* wall-time: 0 d, 0 h, 0 min, 0.137 sec
* cpu-time: 0 d, 0 h, 0 min, 1.080 sec
* ratio c/w: 7.863 speedup
ANC optimizer:
* wall-time: 0 d, 0 h, 0 min, 21.016 sec
* cpu-time: 0 d, 0 h, 2 min, 45.117 sec
* ratio c/w: 7.857 speedup
normal termination of xtb
lscpu
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
CPU(s): 16
On-line CPU(s) list: 0-15
Thread(s) per core: 2
Core(s) per socket: 8
Socket(s): 1
NUMA node(s): 1
Vendor ID: GenuineIntel
CPU family: 6
Model: 79
Model name: Intel(R) Core(TM) i7-6900K CPU @ 3.20GHz
Stepping: 1
CPU MHz: 1198.860
CPU max MHz: 4000.0000
CPU min MHz: 1200.0000
BogoMIPS: 6385.72
Virtualization: VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache: 256K
L3 cache: 20480K
NUMA node0 CPU(s): 0-15
Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch cpuid_fault epb cat_l3 cdp_l3 invpcid_single pti intel_ppin ssbd ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap intel_pt xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts md_clear flush_l1d
add caffeine
CRESTify and for neutral structure multiple protomers, no tautomers.
Check protonated forms and tautomerize.
add benchmarks and threaded scaling
- 6 Core
- 44-core
- 128-core
maybe MD, maybe CREST, maybe opt
Add ginseng
-
Add ginseng example
explain temperature, check if temp settings are possible in XTB/CREST -
Discuss PDF
6500_PS_A4.pdf
xtb gfortran-8 compilation on ARM platform
The compilation on ARM (AWS a1.4xlarge) works. Setup on clean system:
- sudo apt update
- sudo apt upgrade
- sudo apt install hardinfo
- sudo apt install htop
- sudo apt install mc
- sudo apt install python3-pip
- sudo pip3 install meson
- sudo pip3 install ninja (fail)
- sudo apt install ninja-build
- sudo apt-get install libblas-dev liblapack-dev
- sudo apt-get install libopenblas-base libopenblas-dev
- sudo apt-get install gfortran-8
- sudo apt-get install gcc-8
- wget https://github.com/grimme-lab/xtb/archive/master.zip
- mkdir xtb_source
- cd xtb_source
- wget https://github.com/grimme-lab/xtb/archive/master.zip
- unzip master.zip
- cd xtb-master
- export OMP_NUM_THREADS=1,1
- export FC=gfortran-8 CC=gcc-8
- meson setup build_gcc --buildtype release -Dla_backend=openblas --warnlevel 0
- ninja -C build_gcc test
- mkdir test
- cd test
- wget https://raw.githubusercontent.com/tobigithub/quantum-xtb/master/input-molecules/C54H30.xyz
- ./xtb C54H30.xyz --opt extreme
The CPU seems to be of an older type (Cortex-A72), while the new Graviton CPUs are much faster.
See CoreMark https://www.eembc.org/coremark/scores.php the Cortex-A72 (446 sec) is roughly 20-fold slower than a modern Intel Xeon with AVX2 vector instructions (21 seconds).
lscpu
Architecture: aarch64
Byte Order: Little Endian
CPU(s): 16
On-line CPU(s) list: 0-15
Thread(s) per core: 1
Core(s) per socket: 4
Socket(s): 4
NUMA node(s): 1
Vendor ID: ARM
Model: 3
Model name: Cortex-A72
Stepping: r0p3
BogoMIPS: 166.66
L1d cache: 32K
L1i cache: 48K
L2 cache: 2048K
NUMA node0 CPU(s): 0-15
Flags: fp asimd evtstrm aes pmull sha1 sha2 crc32 cpuid
export OMP_NUM_THREADS=1,1
~/xtb_source/test/C54H30-openblas-normal$ ./xtb C54H30.xyz --opt extreme
optimized geometry written to: xtbopt.xyz
-------------------------------------------------
| TOTAL ENERGY -131.025242619724 Eh |
| GRADIENT NORM 0.000032027127 Eh/α |
| HOMO-LUMO GAP 2.139603091690 eV |
-------------------------------------------------
------------------------------------------------------------------------
* finished run on 2020/03/21 at 04:19:23.787
------------------------------------------------------------------------
total:
* wall-time: 0 d, 0 h, 7 min, 26.306 sec
* cpu-time: 0 d, 0 h, 7 min, 26.296 sec
* ratio c/w: 1.000 speedup
SCF:
* wall-time: 0 d, 0 h, 0 min, 1.171 sec
* cpu-time: 0 d, 0 h, 0 min, 1.171 sec
* ratio c/w: 1.000 speedup
ANC optimizer:
* wall-time: 0 d, 0 h, 7 min, 24.886 sec
* cpu-time: 0 d, 0 h, 7 min, 24.876 sec
* ratio c/w: 1.000 speedup
normal termination of xtb
Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG
add PMW dataset
- Discuss diverse 1200 compound opts
- Compare XTB coordinates vs b3lyp/tzvp with overlay (find xyz overlay RMS code)
- Compare energies
- check Inchikey and connection tables, report errors (check NO2, NO3, SO4, dissociations etc)
Maybe use XYZ and MOL route, maybe retain connection table (check old discussions)
Add LEU-ENK
-
Leu-enkephalin
check protomer and sodiated form first, then check tautomers.
check tautomers for normal form. -
Add refs
Investigation of protonated and sodiated leucineenkephalin by hydrogen/deuterium exchange and
theoretical calculations
https://pubs.rsc.org/--/content/getauthorversionpdf/C5AY00684H -
Copy from cluster (30 min?) MOL file 3766
3766.zip
create docker and singularity solution for xtb
Check how to create docker and singularity solution for xtb.
Discuss how it could be officially hosted.
gcc compilation of xtb
compilation of gcc on ubuntu
(VM instance on GCP)
Compilation can be done with meson/ninja, or with make/cmake. Here is the complete installation procedure from a blank system.
Welcome to Ubuntu 18.04.4 LTS (GNU/Linux 5.0.0-1031-gcp x86_64)
>sudo apt-get update
>sudo apt update
>sudo apt upgrade
The refer to build instructions:
https://xtb-docs.readthedocs.io/en/latest/development.html
- Install pip3, ninja and meson, be aware meson and ninja in this case are installed via pip3 not natively (apt install meson) on the OS level. In the case below, without the sudo command meson is installed into "~/.local/bin/meson". See mesonbuild/meson#1613 and https://mesonbuild.com/Quick-guide.html
>sudo apt install python3-pip
>sudo pip3 install meson
>sudo pip3 install ninja
>pip3 list
meson (0.53.2)
ninja (1.9.0.post1)
- Install the BLAS libraries under Ubuntu, if openblas is not installed it may raise an error "ERROR: Fortran library 'openblas' not found"
>sudo apt-get install libblas-dev liblapack-dev
>sudo apt-get install libopenblas-base libopenblas-dev
- Install gcc and gfortran (latest >8.x)
see https://www.osradar.com/install-gnu-fortran-on-ubuntu-18-04/
the normal "sudo apt-get install gfortran" only installs gfortran 7.5 hence we need gfortran-8
this can also be confirmed by looking into the xtb repository
>sudo apt-get install gfortran-8
>sudo apt-get install gcc-8
>gfortran-8 --version
GNU Fortran (Ubuntu 8.3.0-26ubuntu1~18.04) 8.3.0
- get the xtb sources, with wget on gets the master.zip (Windows gets xtb-master)
>mkdir xtb_source
>cd xtb_source
>wget https://codeload.github.com/grimme-lab/xtb/zip/master/xtb-master.zip
>unzip master.zip
>cd xtb-master
- make changes to the system and then built (UBUNTU gcc), openblas backend is defined here, example for netlib see below.
https://github.com/grimme-lab/xtb/blob/master/meson_options.txt also see mesonbuild/meson#4890
>export FC=gfortran-8 CC=gcc-8
>meson setup build_gcc --buildtype release -Dla_backend=openblas --warnlevel 0
>ninja -C build_gcc test
- After running ninja with the tests, a number of warnings may occur, not sure if relevant or not or covered by the tests. Compile time on one Intel Xeon core (2.4 Ghz) is around 1-2 minutes.
[345/365] Compiling Fortran object 'TESTSUITE/477912c@@xtb_test@exe/assertion.f90.o'.
../TESTSUITE/assertion.f90:2:20:
use, intrinsic :: iso_fortran_env
1
Warning: Use of the NUMERIC_STORAGE_SIZE named constant from intrinsic module ISO_FORTRAN_ENV at (1) is incompatible with option -fdefault-real-8
[353/365] Linking target xtb.
/usr/bin/ld: warning: libgfortran.so.4, needed by /usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu/libopenblas.so, may conflict with libgfortran.so.5
[364/365] Linking target TESTSUITE/xtb_test.
/usr/bin/ld: warning: libgfortran.so.4, needed by /usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu/libopenblas.so, may conflict with libgfortran.so.5
[364/365] Running all tests.
1/63 Argparser: print version OK 0.01 s
2/63 Argparser: print help OK 0.01 s
3/63 Argparser: print license OK 0.01 s
4/63 Argparser: no arguments EXPECTEDFAIL 0.02 s
5/63 Info OK 0.01 s
6/63 Singlepoint OK 0.12 s
7/63 Geometry opt. OK 0.37 s
8/63 IP/EA OK 0.17 s
9/63 GFN0-xTB OK 0.07 s
10/63 GFN1-xTB OK 0.12 s
11/63 GFN2-xTB/GBSA OK 0.12 s
12/63 Molecule: axis OK 0.01 s
13/63 Molecule: MIC OK 0.01 s
14/63 Wigner-Seitz Cell (3D) OK 0.01 s
15/63 coord 3D OK 0.01 s
16/63 coord 3D OK 0.01 s
17/63 coord 2D SKIP 0.01 s
18/63 coord 1D SKIP 0.01 s
19/63 coord 0D OK 0.01 s
20/63 Xmol 0D OK 0.01 s
21/63 POSCAR OK 0.01 s
22/63 molfile OK 0.01 s
23/63 molfile flat EXPECTEDFAIL 0.02 s
24/63 SDF OK 0.01 s
25/63 SDF flat EXPECTEDFAIL 0.02 s
26/63 SDF no H EXPECTEDFAIL 0.02 s
27/63 PDB OK 0.01 s
28/63 PDB no H EXPECTEDFAIL 0.02 s
29/63 genFormat OK 0.01 s
30/63 PBC tools: convert OK 0.01 s
31/63 PBC tools: cutoff OK 0.01 s
32/63 Symmetry: Water OK 0.01 s
33/63 Symmetry: Li8 OK 0.01 s
34/63 Symmetry: PCl3 OK 0.01 s
35/63 Symmetry: large OK 0.17 s
36/63 Thermo: axis OK 0.01 s
37/63 Thermo: calculation OK 0.01 s
38/63 Thermo: print OK 0.01 s
39/63 EEQ model: water OK 0.01 s
40/63 EEQ model: 3D Ewald OK 0.01 s
41/63 EEQ model: GBSA OK 0.01 s
42/63 EEQ model: GBSA (salt) OK 0.01 s
43/63 EEQ model: GBSA (H-bond) SKIP 0.01 s
44/63 Dispersion: properties OK 0.02 s
45/63 Dispersion: energies OK 0.02 s
46/63 Dispersion: energies (PBC) OK 1.72 s
47/63 Dispersion: API OK 0.03 s
48/63 GFN2-xTB: SCC OK 0.02 s
49/63 GFN2-xTB: API OK 0.02 s
50/63 GFN2-xTB: API (GBSA) OK 0.03 s
51/63 GFN2-xTB: API (GBSA+salt) OK 0.03 s
52/63 GFN2-xTB: API (PCEM) OK 0.03 s
53/63 GFN1-xTB: SCC OK 0.01 s
54/63 GFN1-xTB: API OK 0.02 s
55/63 GFN1-xTB: XB OK 0.02 s
56/63 GFN1-xTB: API (GBSA) OK 0.02 s
57/63 GFN1-xTB: API (PCEM) OK 0.03 s
58/63 GFN0-xTB: SP OK 0.03 s
59/63 GFN0-xTB: API OK 0.03 s
60/63 GFN0-xTB: SRB OK 0.03 s
61/63 GFN0-xTB: SP (PBC) OK 0.07 s
62/63 GFN0-xTB: API (PBC) OK 0.03 s
63/63 GFN0-xTB: SRB (PBC) OK 0.17 s
Ok: 55
Expected Fail: 5
Fail: 0
Unexpected Pass: 0
Skipped: 3
Timeout: 0
Full log written to /home/tkind/xtb_source/xtb-master/build_gcc/meson-logs/testlog.txt
tkind@instance-1:~/xtb_source/xtb-master$
- Then copy the xtb binary from the folder "/xtb_source/xtb-master/build_gcc/" and run a version test and run a caffeine test.
tkind@instance-1:~/xtb_source/test/caffeine$ ./xtb --version
-----------------------------------------------------------
| ===================== |
| x T B |
| ===================== |
| S. Grimme |
| Mulliken Center for Theoretical Chemistry |
| University of Bonn |
-----------------------------------------------------------
* xtb version 6.2.3 (unknown) compiled by 'tkind@instance-1' on 2020-03-20
normal termination of xtb
tkind@instance-1:~/xtb_source/test/caffeine$
- Now testing the xtb computations whith caffeine as example:
>cat caffeine.ccord
$coord
2.02799738646442 0.09231312124713 -0.14310895950963 C
4.75011007621000 0.02373496014051 -0.14324124033844 N
6.33434307654413 2.07098865582721 -0.14235306905930 C
8.72860718071825 1.38002919517619 -0.14265542523943 N
8.65318821103610 -1.19324866489847 -0.14231527453678 C
6.23857175648671 -2.08353643730276 -0.14218299370797 C
5.63266886875962 -4.69950321056008 -0.13940509630299 C
3.44931709749015 -5.48092386085491 -0.14318454855466 O
7.77508917214346 -6.24427872938674 -0.13107140408805 N
10.30229550927022 -5.39739796609292 -0.13672168520430 C
12.07410272485492 -6.91573621641911 -0.13666499342053 O
10.70038521493902 -2.79078533715849 -0.14148379504141 N
13.24597858727017 -1.76969072232377 -0.14218299370797 C
7.40891694074004 -8.95905928176407 -0.11636933482904 C
1.38702118184179 2.05575746325296 -0.14178615122154 H
1.34622199478497 -0.86356704498496 1.55590600570783 H
1.34624089204623 -0.86133716815647 -1.84340893849267 H
5.65596919189118 4.00172183859480 -0.14131371969009 H
14.67430918222276 -3.26230980007732 -0.14344911021228 H
13.50897177220290 -0.60815166181684 1.54898960808727 H
13.50780014200488 -0.60614855212345 -1.83214617078268 H
5.41408424778406 -9.49239668625902 -0.11022772492007 H
8.31919801555568 -9.74947502841788 1.56539243085954 H
8.31511620712388 -9.76854236502758 -1.79108242206824 H
$end
- running xtb (just copied into the same folder, observe the binaries and config files and folders when transferring)
>./xtb --opt extreme caffeine.coord
...
optimized geometry written to: xtbopt.coord
-------------------------------------------------
| TOTAL ENERGY -42.153937410501 Eh |
| GRADIENT NORM 0.000011578351 Eh/α |
| HOMO-LUMO GAP 3.424625518833 eV |
-------------------------------------------------
------------------------------------------------------------------------
* finished run on 2020/03/20 at 03:39:39.545
------------------------------------------------------------------------
total:
* wall-time: 0 d, 0 h, 0 min, 0.767 sec
* cpu-time: 0 d, 0 h, 0 min, 0.720 sec
* ratio c/w: 0.940 speedup
SCF:
* wall-time: 0 d, 0 h, 0 min, 0.041 sec
* cpu-time: 0 d, 0 h, 0 min, 0.037 sec
* ratio c/w: 0.907 speedup
ANC optimizer:
* wall-time: 0 d, 0 h, 0 min, 0.687 sec
* cpu-time: 0 d, 0 h, 0 min, 0.657 sec
* ratio c/w: 0.957 speedup
normal termination of xtb
Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
Comparing with INTEL compilers and MKL
gcc+gfortran-8 (openblas)
-------------------------------------------------
| TOTAL ENERGY -42.153937410494 Eh |
| GRADIENT NORM 0.000011585590 Eh/a |
| HOMO-LUMO GAP 3.424625890456 eV |
-------------------------------------------------
intel (MKL)
-------------------------------------------------
| TOTAL ENERGY -42.153937383304 Eh |
| GRADIENT NORM 0.000043689684 Eh/a |
| HOMO-LUMO GAP 3.424638764696 eV |
-------------------------------------------------
Difference is 0.00000002719 Eh
Basically the difference between the INTEL compiler and gcc is 0.00000002719 Eh which translates into 0.000017 kcal/mol or a very small error however the IEEE_UNDERFLOW_FLAG IEEE_DENORMAL is somewhat unsettling, reminding me of Intel 387 coprocessor testing times. A quick google search reveals that there are potential remedies to this warning, which I will not explore.
Verdict compiling xtb with gcc and gfortran-8 works.
cuby4 interface examples
Add cuby4 interface examples.
http://cuby4.molecular.cz/interface_xtb.html
time cuby4 dataset_example_02.yaml --parallel 8 --job_cleanup no
_______
/\______\
/ / /
/ / Cuby / Dataset calculation
\/______/
==========================================================================================
name E Eref error error(%)
------------------------------------------------------------------------------------------
01 methane ... F2 -0.137 -0.491 0.354 72.041
02 methane ... Cl2 -0.592 -1.079 0.487 45.146
03 methane ... Br2 -0.860 -1.300 0.440 33.880
04 methane ... I2 -1.117 -1.346 0.229 17.014
05 fluoromethane ... methane -0.536 -0.751 0.215 28.629
06 chloromethane ... methane -0.750 -0.980 0.230 23.446
07 trifluoromethane ... methane -0.764 -0.691 -0.073 -10.632
08 trichloromethane ... methane -1.321 -1.146 -0.175 -15.262
09 fluoromethane dimer -1.341 -1.648 0.307 18.630
10 chloromethane dimer -1.098 -1.338 0.240 17.948
11 trifluorobenzene ... benzene -4.994 -4.405 -0.589 -13.379
12 hexafuorobenzene ... benzene -6.697 -6.121 -0.576 -9.406
13 chloromethane ... formaldehyde -0.252 -1.170 0.918 78.468
14 bromomethane ... formaldehyde 0.011 -1.722 1.733 100.648
15 iodomethane ... formaldehyde -1.489 -2.382 0.893 37.498
16 trifluorochloromethane ... formald... -1.319 -2.246 0.927 41.260
17 trifluorobromomethane ... formalde... -2.475 -3.103 0.628 20.226
18 trifluoroiodomethane ... formaldehyde -5.356 -4.080 -1.276 -31.264
19 chlorobenzene ... acetone -0.647 -1.489 0.842 56.563
20 bromobenzene ... acetone -0.597 -2.426 1.829 75.398
21 iodobenzene ... acetone -2.926 -3.460 0.534 15.445
22 chlorobenzene ... trimethylamine -0.941 -2.113 1.172 55.479
23 bromobenzene ... trimethylamine -1.212 -3.778 2.566 67.923
24 iodobenzene ... trimethylamine -4.070 -5.807 1.737 29.905
25 bromobenzene ... methanethiol -1.037 -2.316 1.279 55.205
26 iodobenzene ... methanethiol -1.837 -3.078 1.241 40.321
27 bromomethane ... benzene -0.885 -1.814 0.929 51.208
28 iodomethane ... benzene -1.686 -2.483 0.797 32.116
29 trifluorobromomethane ... benzene -1.822 -3.110 1.288 41.406
30 trifluoroiodomethane ... benzene -3.544 -3.915 0.371 9.483
31 trifluoromethanol ... water -10.218 -9.669 -0.549 -5.674
32 trichloromethanol ... water -10.062 -10.405 0.343 3.300
33 HF ... methanol -9.477 -9.593 0.116 1.211
34 HCl ... methanol -6.308 -6.300 -0.008 -0.125
35 HBr ... methanol -7.479 -5.356 -2.123 -39.637
36 HI ... methanol -6.223 -3.971 -2.252 -56.700
37 HF ... methylamine -13.265 -14.318 1.053 7.357
38 HCl ... methylamine -10.815 -11.419 0.604 5.290
39 methanol ... fluoromethane -2.622 -3.893 1.271 32.654
40 methanol ... chloromethane -2.704 -3.778 1.074 28.416
==========================================================================================
RMSE 1.062 kcal/mol
MUE 0.857 kcal/mol
------------------------------------------------------------------------------------------
MSE 0.476 kcal/mol
min -2.252 kcal/mol
max 2.566 kcal/mol
range 4.818 kcal/mol
min abs 0.008 kcal/mol
max abs 2.566 kcal/mol
==========================================================================================
RMSE 40.843 %
MUE 33.140 %
MSE 24.036 %
min -56.700 %
max 100.648 %
range 157.348 %
min abs 0.125 %
max abs 100.648 %
------------------------------------------------------------------------------------------
RMSE/|avg| 28.235 %
MUE/|avg| 22.771 %
==========================================================================================
Statistics for groups:
dispersion (4) RMSE 0.390 MSE 0.378 kcal/mol
induction (4) RMSE 0.184 MSE 0.049 kcal/mol
dipole_dipole (2) RMSE 0.276 MSE 0.274 kcal/mol
stack (2) RMSE 0.583 MSE -0.583 kcal/mol
X-bond (14) RMSE 1.363 MSE 1.073 kcal/mol
X-pi (4) RMSE 0.908 MSE 0.846 kcal/mol
H-bond (10) RMSE 1.194 MSE -0.047 kcal/mol
--------------------------------------------------------------------------------
dispersion RMSE/|avg| 37.02 %
induction RMSE/|avg| 20.60 %
dipole_dipole RMSE/|avg| 18.46 %
stack RMSE/|avg| 11.07 %
X-bond RMSE/|avg| 48.72 %
X-pi RMSE/|avg| 32.06 %
H-bond RMSE/|avg| 15.17 %
==========================================================================================
Add aniline
- Discuss XTB CREST results for aniline, check why 4 tautomers are reported instead of three.
============= ordered structure list ==============
===================================================
written to file <tautomers.xyz>
structure ΔE(kcal/mol) Etot(Eh)
1 0.00 -19.316692
2 26.60 -19.274309
3 26.60 -19.274309
4 27.52 -19.272836
-
Add refs from ion mobility
-
Characterizing the Tautomers of Protonated Aniline UsingDifferential Mobility Spectrometry and Mass Spectrometry
https://pubs.acs.org/doi/pdf/10.1021/acs.jpca.7b10872 -
A Mechanistic Study of Protonated Aniline to Protonated Phenol Substitution Considering Tautomerization by Ion Mobility Mass Spectrometry and Tandem Mass Spectrometry
https://pubs.acs.org/doi/pdf/10.1021/jasms.8b06259
14
N 1.33368 3.85000 0.00000
C 1.33368 2.31000 0.00000
C 2.66736 1.54000 0.00000
C 2.66736 -0.00000 0.00000
C 1.33368 -0.77000 0.00000
C 0.00000 0.00000 0.00000
C 0.00000 1.54000 0.00000
H 2.66736 4.62000 0.00000
H 0.00000 4.62000 0.00000
H 4.00104 2.31000 0.00000
H 4.00104 -0.77000 0.00000
H 1.33368 -2.31000 0.00000
H -1.33368 -0.77000 0.00000
H -1.33368 2.31000 0.00000
add sodiated alanylglycine
-
Crest can handle sodium adducts
Check vs classical tools -
Check and display
Source: https://cactus.nci.nih.gov/tautomerizer/
Input: "CC@HC(\NCC(O)=O)=[O+]/[Na]" -
Discuss output from CREST for Sodium-adduct-1.xyz
Discuss implications for IM and MS
===================================================
============= ordered structure list ==============
===================================================
written to file <tautomers.xyz>
structure ΔE(kcal/mol) Etot(Eh)
1 0.00 -34.133685
2 12.39 -34.113939
3 13.43 -34.112288
4 14.41 -34.110724
5 15.19 -34.109483
6 17.07 -34.106490
7 20.99 -34.100235
8 21.00 -34.100227
9 22.74 -34.097449
10 24.04 -34.095383
11 24.04 -34.095383
12 24.08 -34.095314
13 24.40 -34.094808
14 25.20 -34.093519
15 25.48 -34.093082
16 25.48 -34.093082
17 25.53 -34.092996
18 25.61 -34.092866
19 25.73 -34.092684
20 26.11 -34.092078
21 26.94 -34.090758
22 27.59 -34.089719
23 28.58 -34.088138
24 28.62 -34.088082
25 28.76 -34.087847
26 28.76 -34.087847
27 29.19 -34.087167
28 29.44 -34.086769
Check additional protomers.
add C6H6 series
add C6H6 series
- with xyz2mol errors
- with direct MOL file handling and INCHIKEY check
Create WIKI sidebar
Create WIKI sidebar
xtb gfortran-8 compilation on ARM architecture
AWS instance a1.4xlarge
Add olestra GBSA for multiple solvents
Use runall-solvents.sh
Olestra GBSA optimization only works with
ulimit -s unlimited
xtb on AWS Graviton2
Check AWS Graviton2 64 c6g.16xlarge (64-bit Arm Neoverse N1) vCPU lscpu using Ubuntu
lscpu
Architecture: aarch64
Byte Order: Little Endian
CPU(s): 64
On-line CPU(s) list: 0-63
Thread(s) per core: 1
Core(s) per socket: 64
Socket(s): 1
NUMA node(s): 1
Vendor ID: ARM
Model: 1
Stepping: r3p1
BogoMIPS: 243.75
L1d cache: 64K
L1i cache: 64K
L2 cache: 1024K
L3 cache: 32768K
NUMA node0 CPU(s): 0-63
Flags: fp asimd evtstrm aes pmull sha1 sha2 crc32 atomics fphp asimdhp cpuid
asimdrdm lrcpc dcpop asimddp ssbs
For compilation of the xtb code on AWS Graviton and Graviton2 see here #21
In terms of performance it is important to use proper OMP directives such as seen here. If these are not included, calculations that take 20 seconds will last for >2 hours. OMP bind directives include:
export OMP_STACKSIZE=1G
export OMP_PLACES=cores
export OMP_PROC_BIND=spread
export OMP_NUM_THREADS=32,1
Timing results with command
./xtb C54H30.xyz --opt extreme
export OMP_NUM_THREADS=1,1 : 45 sec
export OMP_NUM_THREADS=2,1 : 29 sec
export OMP_NUM_THREADS=4,1 : 24 sec
export OMP_NUM_THREADS=8,1 : 25 sec
export OMP_NUM_THREADS=16,1 : 22 sec
export OMP_NUM_THREADS=32,1 : 22 sec
export OMP_NUM_THREADS=64,1 : 26 sec
Threads are not running at 100%, could be cache or memory bottleneck.
This behavior can be changed with the OMP directive https://www.openmp.org/spec-html/5.0/openmpse55.html#x294-20640006.7 when running on all 64 cores, however the benchmark times are unchanged.
export OMP_WAIT_POLICY=active
Add fullerenes
Add cases and files for fullerenes, also use xtb-discussion about SDF data and figure
Add Tian Lu (sobereva) gaussian xtb interface
update readme
- Add link to WIKI
- Picture
- refs maybe
Add Windows installation and use (WSL)
Check and transfer files.
Add waterbox for CREST
Add water box and or multiple solvent molecules for CREST
compare energies, check MD
Find paper with DFT that did the same.
WIKI figures
Place holder for WIKI figures
Figure INTRO:
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