merging stable and exaalt branches into exaaltstable (7b1542a0) · Commits · 郑智淋 / lammps

.gitlab-ci.yml

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		image: ubuntu:latest

		test:

		before_script:

		# Install Linux Packages:
		- apt-get update
		- hostname
		- export HOME=/builds/exaalt/
		- env
		- apt-get --yes --force-yes install gfortran libblas-dev liblapack-dev
		- apt-get --yes --force-yes install cmake python gcc cmake-data g++ git wget
		- apt-get --yes --force-yes install pkg-config python-numpy python3-numpy libopenmpi-dev

		# Build LATTE:
		- cd /builds/exaalt/
		- git clone https://github.com/lanl/LATTE.git
		- cd LATTE
		- cp ./makefiles/makefile.CHOICES.gfort.lapack.lmp makefile.CHOICES
		- make

		# Build LAMMPS:
		- cd /builds/exaalt/lammps/lib/latte/
		- cp Makefile.lammps.gfortran Makefile.lammps
		- cd /builds/exaalt/lammps/src/
		- make yes-latte
		- make yes-molecule
		- make serial

		script:

		# Test LAMMPS-LATTE Example:
		- cd /builds/exaalt/lammps/examples/latte/
		- ../../src/lmp_serial -in in.latte.water

examples/latte/TBparam/bondints.nonortho

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		Noints= 34
		Element1 Element2 Kind H0 B1 B2 B3 B4 B5 R1 Rcut H0 B1 B2 B3 B4 B5 R1 Rcut
		N O sss -11.430028 -2.257346 -1.152844 0.000000 0.000000 1.200000 3.500000 4.000000 0.340064 -1.703613 -0.622348 0.036738 -0.040158 1.200000 3.500000 4.000000
		N O sps 11.597479 -1.382001 -0.765170 0.000000 0.000000 1.200000 3.500000 4.000000 -0.370946 -1.040947 -0.931097 0.252441 -0.115450 1.200000 3.500000 4.000000
		O N sps 12.143744 -0.822913 -0.676127 0.000000 0.000000 1.200000 3.500000 4.000000 -0.420014 -1.107918 -0.905594 0.188424 -0.088365 1.200000 3.500000 4.000000
		N O pps 9.465191 -1.082032 -0.769214 0.000000 0.000000 1.200000 3.500000 4.000000 -0.314073 0.499050 -2.914288 2.067657 -0.738439 1.200000 3.500000 4.000000
		N O ppp -4.676789 -2.171480 -0.288002 0.000000 0.000000 1.200000 3.500000 4.000000 0.223937 -1.991867 -0.537630 -0.081270 -0.004130 1.200000 3.500000 4.000000
		C O sss -14.369472 -2.077439 -0.875471 0.000000 0.000000 1.200000 3.500000 4.000000 0.375339 -1.547372 -0.642492 0.020614 -0.026699 1.200000 3.500000 4.000000
		C O sps 9.576296 -1.156217 -0.494803 0.000000 0.000000 1.200000 3.500000 4.000000 -0.373027 -0.776043 -1.019920 0.257539 -0.102838 1.200000 3.500000 4.000000
		O C sps 14.037374 -1.192632 -0.654572 0.000000 0.000000 1.200000 3.500000 4.000000 -0.458068 -1.035067 -0.937868 0.190562 -0.077841 1.200000 3.500000 4.000000
		C O pps 9.331152 -0.718120 -0.822100 0.000000 0.000000 1.200000 3.500000 4.000000 -0.322293 0.795473 -3.476601 2.589965 -0.897800 1.200000 3.500000 4.000000
		C O ppp -5.334367 -2.263939 -0.204910 0.000000 0.000000 1.200000 3.500000 4.000000 0.244570 -1.922717 -0.573671 -0.057280 -0.004108 1.200000 3.500000 4.000000
		C N sss -7.010061 -1.730597 -0.575559 0.000000 0.000000 1.500000 3.500000 4.000000 0.263438 -1.754525 -0.584215 -0.007801 -0.021729 1.500000 3.500000 4.000000
		C N sps 7.543283 -1.293768 -0.624363 0.000000 0.000000 1.500000 3.500000 4.000000 -0.326609 -1.197485 -0.807786 0.134891 -0.084373 1.500000 3.500000 4.000000
		N C sps 9.090970 -1.494255 -0.616711 0.000000 0.000000 1.500000 3.500000 4.000000 -0.337943 -1.335442 -0.769693 0.119373 -0.079493 1.500000 3.500000 4.000000
		C N pps 6.892240 -0.931920 -0.769164 0.000000 0.000000 1.500000 3.500000 4.000000 -0.350240 -0.467439 -1.849316 1.854403 -0.988471 1.500000 3.500000 4.000000
		C N ppp -2.903346 -2.149349 -0.253006 0.000000 0.000000 1.500000 3.500000 4.000000 0.158424 -2.114409 -0.582346 -0.051076 -0.006183 1.500000 3.500000 4.000000
		C C sss -9.404207 -1.363297 -0.507128 0.000000 0.000000 1.400000 3.500000 4.000000 0.346977 -1.519820 -0.570812 -0.013518 -0.015829 1.400000 3.500000 4.000000
		C C sps 8.662429 -1.047410 -0.661999 0.000000 0.000000 1.400000 3.500000 4.000000 -0.400467 -0.984048 -0.853949 0.157178 -0.073381 1.400000 3.500000 4.000000
		C C pps 6.811512 -0.552299 -0.776890 0.000000 0.000000 1.400000 3.500000 4.000000 -0.382417 0.102889 -2.786680 2.646356 -1.134320 1.400000 3.500000 4.000000
		C C ppp -3.550127 -1.925572 -0.132715 0.000000 0.000000 1.400000 3.500000 4.000000 0.214357 -1.948923 -0.578323 -0.034356 -0.007257 1.400000 3.500000 4.000000
		H C sss -9.072577 -1.393093 -0.430611 0.000000 0.000000 1.100000 3.500000 4.000000 0.416003 -1.459596 -0.654874 0.009140 -0.012658 1.100000 3.500000 4.000000
		H C sps 8.176008 -0.985177 -0.427403 0.000000 0.000000 1.100000 3.500000 4.000000 -0.495695 -0.901626 -1.007214 0.189808 -0.057087 1.100000 3.500000 4.000000
		H H sss -9.340000 -1.145903 -0.391777 0.000000 0.000000 0.750000 3.500000 4.000000 0.575007 -1.391261 -0.778831 0.080209 -0.017759 0.750000 3.500000 4.000000
		O O sss -12.737687 -1.851608 -0.666621 0.000000 0.000000 1.200000 3.500000 4.000000 0.296445 -1.911896 -0.663451 0.038054 -0.046608 1.200000 3.500000 4.000000
		O O sps 13.683050 -1.684554 -0.468349 0.000000 0.000000 1.200000 3.500000 4.000000 -0.362143 -1.285274 -0.939591 0.204641 -0.106438 1.200000 3.500000 4.000000
		O O pps 9.460772 -1.211748 -0.581016 0.000000 0.000000 1.200000 3.500000 4.000000 -0.312044 0.121814 -2.519352 1.681266 -0.644566 1.200000 3.500000 4.000000
		O O ppp -4.494595 -2.709223 -0.284124 0.000000 0.000000 1.200000 3.500000 4.000000 0.193010 -2.168462 -0.580629 -0.105104 0.004891 1.200000 3.500000 4.000000
		H O sss -12.230931 -1.808632 -0.421164 0.000000 0.000000 1.000000 3.500000 4.000000 0.404725 -1.702546 -0.707938 0.074904 -0.039922 1.000000 3.500000 4.000000
		H O sps 9.466088 -1.321262 -0.386336 0.000000 0.000000 1.000000 3.500000 4.000000 -0.447660 -0.952979 -1.163537 0.400616 -0.156965 1.000000 3.500000 4.000000
		N N sss -7.710330 -2.365312 -0.525527 0.000000 0.000000 1.500000 3.500000 4.000000 0.231654 -1.879002 -0.572765 -0.004579 -0.031106 1.500000 3.500000 4.000000
		N N sps 8.222314 -1.612118 -0.690081 0.000000 0.000000 1.500000 3.500000 4.000000 -0.305271 -1.385158 -0.751032 0.114531 -0.090839 1.500000 3.500000 4.000000
		N N pps 7.178570 -1.176467 -0.571049 0.000000 0.000000 1.500000 3.500000 4.000000 -0.324668 -0.547805 -1.638658 1.495168 -0.827868 1.500000 3.500000 4.000000
		N N ppp -2.829344 -2.408049 -0.387709 0.000000 0.000000 1.500000 3.500000 4.000000 0.142909 -2.162036 -0.571942 -0.071640 -0.004682 1.500000 3.500000 4.000000
		H N sss -12.095890 -1.519057 -0.277247 0.000000 0.000000 1.000000 3.500000 4.000000 0.446693 -1.500463 -0.657448 0.065741 -0.037004 1.000000 3.500000 4.000000
		H N sps 9.851338 -1.231616 -0.370836 0.000000 0.000000 1.000000 3.500000 4.000000 -0.501530 -0.785734 -1.123232 0.394878 -0.148501 1.000000 3.500000 4.000000

examples/latte/TBparam/electrons.dat

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Original line number	Diff line number	Diff line
		Noelem= 5
		Element basis Numel Es Ep Ed Ef Mass HubbardU Wss Wpp Wdd Wff
		N sp 5.0 -18.58 -7.09 0.0 0.0 14.0067 15.93 0.0 -0.6950 0.0 0.0
		O sp 6.0 -23.96 -9.02 0.0 0.0 15.9994 12.15 0.0 -0.7577 0.0 0.0
		H s 1.0 -6.35 0.0 0.0 0.0 1.0079 12.85 -1.7937 0.0 0.0 0.0
		C sp 4.0 -13.75 -5.28 0.0 0.0 12.01 10.0 0.0 -0.621 0.0 0.0
		Ti sd 4.0 -5.5 0.0 -3.0 0.0 47.867 10.0 0.0 0.0 0.0 0.0
		No newline at end of file

examples/latte/TBparam/ppots.nonortho

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Original line number	Diff line number	Diff line
		Nopps= 10
		Ele1 Ele2 A0 A1 A2 A3 A4 A5 A6 C R1 Rcut
		N O 13.182426 20.050322 -46.806321 38.206953 -12.319656 0.000000 0.000000 0.000000 1.600000 1.700000
		C N 88.953762 10.294988 -27.706877 22.101434 -6.836438 0.000000 0.000000 0.000000 1.600000 1.700000
		C O 0.944093 30.116337 -59.608215 45.107654 -13.178839 0.000000 0.000000 0.000000 1.600000 1.700000
		C H 104.889589 3.971095 -23.823043 26.408093 -11.317522 0.000000 0.000000 0.000000 1.200000 1.300000
		C C 3.962931 24.467772 -51.156024 39.031644 -11.342979 0.000000 0.000000 0.000000 1.600000 1.700000
		H H 38.512100 3.887860 -37.769100 57.083500 -34.512200 0.000000 0.000000 0.000000 0.900000 1.000000
		N N 43.228899 15.004605 -36.621777 29.234888 -8.912743 0.000000 0.000000 0.000000 1.600000 1.700000
		N H 0.625470 28.081241 -63.414297 53.286361 -17.352234 0.000000 0.000000 0.000000 1.300000 1.400000
		O O 10.999870 19.303033 -45.747853 37.946431 -11.935755 0.000000 0.000000 0.000000 1.500000 1.600000
		O H 0.481176 33.175383 -81.158683 74.935408 -26.792315 0.000000 0.000000 0.000000 1.200000 1.300000

examples/latte/data.sucrose_non_opt.lmp

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Original line number	Diff line number	Diff line
		LAMMPS Description

		45 atoms

		3 atom types

		0.0000000000000000 18.917000000000002 xlo xhi
		0.0000000000000000 17.350999999999999 ylo yhi
		0.0000000000000000 15.472000000000000 zlo zhi

		Masses

		1 15.994915008544922
		2 12.000000000000000
		3 1.0078250169754028

		Atoms

		1 1 1 0.0 11.47359 7.39174 7.26456
		2 1 2 0.0 12.66159 8.24474 7.53356
		3 1 3 0.0 13.49759 7.72474 7.00656
		4 1 2 0.0 12.92859 8.18374 9.02956
		5 1 1 0.0 13.69659 9.10274 10.46556
		6 1 2 0.0 12.83959 10.10474 6.64056
		7 1 3 0.0 13.24359 10.33074 7.58456
		8 1 1 0.0 13.17359 9.67874 5.60956
		9 1 2 0.0 11.20559 10.26374 6.86456
		10 1 3 0.0 11.22159 11.15674 6.18156
		11 1 1 0.0 10.78559 10.69674 8.19156
		12 1 2 0.0 10.23459 9.20474 6.34356
		13 1 3 0.0 9.23359 9.62574 6.11656
		14 1 1 0.0 10.73959 8.65074 5.08856
		15 1 2 0.0 10.18759 8.08774 7.38056
		16 1 3 0.0 10.03259 8.49174 8.42656
		17 1 1 0.0 9.22959 7.03374 7.08156
		18 1 2 0.0 7.79359 7.27874 7.34356
		19 1 1 0.0 7.44259 8.64274 6.96956
		20 1 2 0.0 7.01059 9.43674 8.13856
		21 1 3 0.0 5.95059 9.74974 7.96256
		22 1 2 0.0 7.08359 8.51474 9.35656
		23 1 3 0.0 8.19359 8.08474 9.80956
		24 1 1 0.0 5.86059 8.56174 10.14056
		25 1 2 0.0 7.34259 7.10674 8.80356
		26 1 3 0.0 6.37259 6.54074 8.80556
		27 1 1 0.0 8.32159 6.38474 9.58156
		28 1 2 0.0 7.89859 10.67174 8.17156
		29 1 1 0.0 6.06859 12.11474 7.59256
		30 1 2 0.0 7.47359 7.05174 5.99256
		31 1 1 0.0 5.66359 6.54374 6.50656
		32 1 3 0.0 12.00659 8.11374 9.61556
		33 1 3 0.0 13.35859 7.21774 9.30856
		34 1 3 0.0 13.67759 8.46774 11.22956
		35 1 3 0.0 12.44459 9.34474 5.00556
		36 1 3 0.0 11.54859 11.18274 8.59756
		37 1 3 0.0 11.00959 7.71574 5.30056
		38 1 3 0.0 5.09459 8.45474 9.52056
		39 1 3 0.0 7.92859 6.23074 10.47756
		40 1 3 0.0 8.53259 10.62974 7.23156
		41 1 3 0.0 8.58159 10.63874 9.05856
		42 1 3 0.0 6.42359 13.37374 7.86056
		43 1 3 0.0 7.58559 6.90074 4.62256
		44 1 3 0.0 7.35159 5.27974 6.61456
		45 1 3 0.0 5.22759 6.18974 5.69256

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