forked from lijiext/lammps
updated fix_langevin and made example
This commit is contained in:
casievers
parent
f4df51763d
commit
4a80edd75f
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@ -0,0 +1,886 @@
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LAMMPS description
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864 atoms
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0 bonds
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0 angles
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0 dihedrals
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0 impropers
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1 atom types
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0 bond types
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0 angle types
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0 dihedral types
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0 improper types
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0.0000000 32.146000 xlo xhi
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0.0000000 32.146000 ylo yhi
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0.0000000 32.146000 zlo zhi
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Atoms
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4 4 1 0.0000000 0.0000000 2.6790000 18.7520000
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5 5 1 0.0000000 0.0000000 2.6790000 24.1090000
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6 6 1 0.0000000 0.0000000 2.6790000 29.4670000
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7 7 1 0.0000000 0.0000000 8.0360000 2.6790000
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8 8 1 0.0000000 0.0000000 8.0360000 8.0360000
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9 9 1 0.0000000 0.0000000 8.0360000 13.3940000
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591 591 1 0.0000000 24.1090000 13.3940000 16.0730000
|
||||
592 592 1 0.0000000 24.1090000 13.3940000 21.4310000
|
||||
593 593 1 0.0000000 24.1090000 13.3940000 26.7880000
|
||||
594 594 1 0.0000000 24.1090000 13.3940000 32.1460000
|
||||
595 595 1 0.0000000 24.1090000 18.7520000 5.3580000
|
||||
596 596 1 0.0000000 24.1090000 18.7520000 10.7150000
|
||||
597 597 1 0.0000000 24.1090000 18.7520000 16.0730000
|
||||
598 598 1 0.0000000 24.1090000 18.7520000 21.4310000
|
||||
599 599 1 0.0000000 24.1090000 18.7520000 26.7880000
|
||||
600 600 1 0.0000000 24.1090000 18.7520000 32.1460000
|
||||
601 601 1 0.0000000 24.1090000 24.1090000 5.3580000
|
||||
602 602 1 0.0000000 24.1090000 24.1090000 10.7150000
|
||||
603 603 1 0.0000000 24.1090000 24.1090000 16.0730000
|
||||
604 604 1 0.0000000 24.1090000 24.1090000 21.4310000
|
||||
605 605 1 0.0000000 24.1090000 24.1090000 26.7880000
|
||||
606 606 1 0.0000000 24.1090000 24.1090000 32.1460000
|
||||
607 607 1 0.0000000 24.1090000 29.4670000 5.3580000
|
||||
608 608 1 0.0000000 24.1090000 29.4670000 10.7150000
|
||||
609 609 1 0.0000000 24.1090000 29.4670000 16.0730000
|
||||
610 610 1 0.0000000 24.1090000 29.4670000 21.4310000
|
||||
611 611 1 0.0000000 24.1090000 29.4670000 26.7880000
|
||||
612 612 1 0.0000000 24.1090000 29.4670000 32.1460000
|
||||
613 613 1 0.0000000 29.4670000 2.6790000 5.3580000
|
||||
614 614 1 0.0000000 29.4670000 2.6790000 10.7150000
|
||||
615 615 1 0.0000000 29.4670000 2.6790000 16.0730000
|
||||
616 616 1 0.0000000 29.4670000 2.6790000 21.4310000
|
||||
617 617 1 0.0000000 29.4670000 2.6790000 26.7880000
|
||||
618 618 1 0.0000000 29.4670000 2.6790000 32.1460000
|
||||
619 619 1 0.0000000 29.4670000 8.0360000 5.3580000
|
||||
620 620 1 0.0000000 29.4670000 8.0360000 10.7150000
|
||||
621 621 1 0.0000000 29.4670000 8.0360000 16.0730000
|
||||
622 622 1 0.0000000 29.4670000 8.0360000 21.4310000
|
||||
623 623 1 0.0000000 29.4670000 8.0360000 26.7880000
|
||||
624 624 1 0.0000000 29.4670000 8.0360000 32.1460000
|
||||
625 625 1 0.0000000 29.4670000 13.3940000 5.3580000
|
||||
626 626 1 0.0000000 29.4670000 13.3940000 10.7150000
|
||||
627 627 1 0.0000000 29.4670000 13.3940000 16.0730000
|
||||
628 628 1 0.0000000 29.4670000 13.3940000 21.4310000
|
||||
629 629 1 0.0000000 29.4670000 13.3940000 26.7880000
|
||||
630 630 1 0.0000000 29.4670000 13.3940000 32.1460000
|
||||
631 631 1 0.0000000 29.4670000 18.7520000 5.3580000
|
||||
632 632 1 0.0000000 29.4670000 18.7520000 10.7150000
|
||||
633 633 1 0.0000000 29.4670000 18.7520000 16.0730000
|
||||
634 634 1 0.0000000 29.4670000 18.7520000 21.4310000
|
||||
635 635 1 0.0000000 29.4670000 18.7520000 26.7880000
|
||||
636 636 1 0.0000000 29.4670000 18.7520000 32.1460000
|
||||
637 637 1 0.0000000 29.4670000 24.1090000 5.3580000
|
||||
638 638 1 0.0000000 29.4670000 24.1090000 10.7150000
|
||||
639 639 1 0.0000000 29.4670000 24.1090000 16.0730000
|
||||
640 640 1 0.0000000 29.4670000 24.1090000 21.4310000
|
||||
641 641 1 0.0000000 29.4670000 24.1090000 26.7880000
|
||||
642 642 1 0.0000000 29.4670000 24.1090000 32.1460000
|
||||
643 643 1 0.0000000 29.4670000 29.4670000 5.3580000
|
||||
644 644 1 0.0000000 29.4670000 29.4670000 10.7150000
|
||||
645 645 1 0.0000000 29.4670000 29.4670000 16.0730000
|
||||
646 646 1 0.0000000 29.4670000 29.4670000 21.4310000
|
||||
647 647 1 0.0000000 29.4670000 29.4670000 26.7880000
|
||||
648 648 1 0.0000000 29.4670000 29.4670000 32.1460000
|
||||
649 649 1 0.0000000 0.0000000 5.3580000 5.3580000
|
||||
650 650 1 0.0000000 0.0000000 5.3580000 10.7150000
|
||||
651 651 1 0.0000000 0.0000000 5.3580000 16.0730000
|
||||
652 652 1 0.0000000 0.0000000 5.3580000 21.4310000
|
||||
653 653 1 0.0000000 0.0000000 5.3580000 26.7880000
|
||||
654 654 1 0.0000000 0.0000000 5.3580000 32.1460000
|
||||
655 655 1 0.0000000 0.0000000 10.7150000 5.3580000
|
||||
656 656 1 0.0000000 0.0000000 10.7150000 10.7150000
|
||||
657 657 1 0.0000000 0.0000000 10.7150000 16.0730000
|
||||
658 658 1 0.0000000 0.0000000 10.7150000 21.4310000
|
||||
659 659 1 0.0000000 0.0000000 10.7150000 26.7880000
|
||||
660 660 1 0.0000000 0.0000000 10.7150000 32.1460000
|
||||
661 661 1 0.0000000 0.0000000 16.0730000 5.3580000
|
||||
662 662 1 0.0000000 0.0000000 16.0730000 10.7150000
|
||||
663 663 1 0.0000000 0.0000000 16.0730000 16.0730000
|
||||
664 664 1 0.0000000 0.0000000 16.0730000 21.4310000
|
||||
665 665 1 0.0000000 0.0000000 16.0730000 26.7880000
|
||||
666 666 1 0.0000000 0.0000000 16.0730000 32.1460000
|
||||
667 667 1 0.0000000 0.0000000 21.4310000 5.3580000
|
||||
668 668 1 0.0000000 0.0000000 21.4310000 10.7150000
|
||||
669 669 1 0.0000000 0.0000000 21.4310000 16.0730000
|
||||
670 670 1 0.0000000 0.0000000 21.4310000 21.4310000
|
||||
671 671 1 0.0000000 0.0000000 21.4310000 26.7880000
|
||||
672 672 1 0.0000000 0.0000000 21.4310000 32.1460000
|
||||
673 673 1 0.0000000 0.0000000 26.7880000 5.3580000
|
||||
674 674 1 0.0000000 0.0000000 26.7880000 10.7150000
|
||||
675 675 1 0.0000000 0.0000000 26.7880000 16.0730000
|
||||
676 676 1 0.0000000 0.0000000 26.7880000 21.4310000
|
||||
677 677 1 0.0000000 0.0000000 26.7880000 26.7880000
|
||||
678 678 1 0.0000000 0.0000000 26.7880000 32.1460000
|
||||
679 679 1 0.0000000 0.0000000 32.1460000 5.3580000
|
||||
680 680 1 0.0000000 0.0000000 32.1460000 10.7150000
|
||||
681 681 1 0.0000000 0.0000000 32.1460000 16.0730000
|
||||
682 682 1 0.0000000 0.0000000 32.1460000 21.4310000
|
||||
683 683 1 0.0000000 0.0000000 32.1460000 26.7880000
|
||||
684 684 1 0.0000000 0.0000000 32.1460000 32.1460000
|
||||
685 685 1 0.0000000 5.3580000 5.3580000 5.3580000
|
||||
686 686 1 0.0000000 5.3580000 5.3580000 10.7150000
|
||||
687 687 1 0.0000000 5.3580000 5.3580000 16.0730000
|
||||
688 688 1 0.0000000 5.3580000 5.3580000 21.4310000
|
||||
689 689 1 0.0000000 5.3580000 5.3580000 26.7880000
|
||||
690 690 1 0.0000000 5.3580000 5.3580000 32.1460000
|
||||
691 691 1 0.0000000 5.3580000 10.7150000 5.3580000
|
||||
692 692 1 0.0000000 5.3580000 10.7150000 10.7150000
|
||||
693 693 1 0.0000000 5.3580000 10.7150000 16.0730000
|
||||
694 694 1 0.0000000 5.3580000 10.7150000 21.4310000
|
||||
695 695 1 0.0000000 5.3580000 10.7150000 26.7880000
|
||||
696 696 1 0.0000000 5.3580000 10.7150000 32.1460000
|
||||
697 697 1 0.0000000 5.3580000 16.0730000 5.3580000
|
||||
698 698 1 0.0000000 5.3580000 16.0730000 10.7150000
|
||||
699 699 1 0.0000000 5.3580000 16.0730000 16.0730000
|
||||
700 700 1 0.0000000 5.3580000 16.0730000 21.4310000
|
||||
701 701 1 0.0000000 5.3580000 16.0730000 26.7880000
|
||||
702 702 1 0.0000000 5.3580000 16.0730000 32.1460000
|
||||
703 703 1 0.0000000 5.3580000 21.4310000 5.3580000
|
||||
704 704 1 0.0000000 5.3580000 21.4310000 10.7150000
|
||||
705 705 1 0.0000000 5.3580000 21.4310000 16.0730000
|
||||
706 706 1 0.0000000 5.3580000 21.4310000 21.4310000
|
||||
707 707 1 0.0000000 5.3580000 21.4310000 26.7880000
|
||||
708 708 1 0.0000000 5.3580000 21.4310000 32.1460000
|
||||
709 709 1 0.0000000 5.3580000 26.7880000 5.3580000
|
||||
710 710 1 0.0000000 5.3580000 26.7880000 10.7150000
|
||||
711 711 1 0.0000000 5.3580000 26.7880000 16.0730000
|
||||
712 712 1 0.0000000 5.3580000 26.7880000 21.4310000
|
||||
713 713 1 0.0000000 5.3580000 26.7880000 26.7880000
|
||||
714 714 1 0.0000000 5.3580000 26.7880000 32.1460000
|
||||
715 715 1 0.0000000 5.3580000 32.1460000 5.3580000
|
||||
716 716 1 0.0000000 5.3580000 32.1460000 10.7150000
|
||||
717 717 1 0.0000000 5.3580000 32.1460000 16.0730000
|
||||
718 718 1 0.0000000 5.3580000 32.1460000 21.4310000
|
||||
719 719 1 0.0000000 5.3580000 32.1460000 26.7880000
|
||||
720 720 1 0.0000000 5.3580000 32.1460000 32.1460000
|
||||
721 721 1 0.0000000 10.7150000 5.3580000 5.3580000
|
||||
722 722 1 0.0000000 10.7150000 5.3580000 10.7150000
|
||||
723 723 1 0.0000000 10.7150000 5.3580000 16.0730000
|
||||
724 724 1 0.0000000 10.7150000 5.3580000 21.4310000
|
||||
725 725 1 0.0000000 10.7150000 5.3580000 26.7880000
|
||||
726 726 1 0.0000000 10.7150000 5.3580000 32.1460000
|
||||
727 727 1 0.0000000 10.7150000 10.7150000 5.3580000
|
||||
728 728 1 0.0000000 10.7150000 10.7150000 10.7150000
|
||||
729 729 1 0.0000000 10.7150000 10.7150000 16.0730000
|
||||
730 730 1 0.0000000 10.7150000 10.7150000 21.4310000
|
||||
731 731 1 0.0000000 10.7150000 10.7150000 26.7880000
|
||||
732 732 1 0.0000000 10.7150000 10.7150000 32.1460000
|
||||
733 733 1 0.0000000 10.7150000 16.0730000 5.3580000
|
||||
734 734 1 0.0000000 10.7150000 16.0730000 10.7150000
|
||||
735 735 1 0.0000000 10.7150000 16.0730000 16.0730000
|
||||
736 736 1 0.0000000 10.7150000 16.0730000 21.4310000
|
||||
737 737 1 0.0000000 10.7150000 16.0730000 26.7880000
|
||||
738 738 1 0.0000000 10.7150000 16.0730000 32.1460000
|
||||
739 739 1 0.0000000 10.7150000 21.4310000 5.3580000
|
||||
740 740 1 0.0000000 10.7150000 21.4310000 10.7150000
|
||||
741 741 1 0.0000000 10.7150000 21.4310000 16.0730000
|
||||
742 742 1 0.0000000 10.7150000 21.4310000 21.4310000
|
||||
743 743 1 0.0000000 10.7150000 21.4310000 26.7880000
|
||||
744 744 1 0.0000000 10.7150000 21.4310000 32.1460000
|
||||
745 745 1 0.0000000 10.7150000 26.7880000 5.3580000
|
||||
746 746 1 0.0000000 10.7150000 26.7880000 10.7150000
|
||||
747 747 1 0.0000000 10.7150000 26.7880000 16.0730000
|
||||
748 748 1 0.0000000 10.7150000 26.7880000 21.4310000
|
||||
749 749 1 0.0000000 10.7150000 26.7880000 26.7880000
|
||||
750 750 1 0.0000000 10.7150000 26.7880000 32.1460000
|
||||
751 751 1 0.0000000 10.7150000 32.1460000 5.3580000
|
||||
752 752 1 0.0000000 10.7150000 32.1460000 10.7150000
|
||||
753 753 1 0.0000000 10.7150000 32.1460000 16.0730000
|
||||
754 754 1 0.0000000 10.7150000 32.1460000 21.4310000
|
||||
755 755 1 0.0000000 10.7150000 32.1460000 26.7880000
|
||||
756 756 1 0.0000000 10.7150000 32.1460000 32.1460000
|
||||
757 757 1 0.0000000 16.0730000 5.3580000 5.3580000
|
||||
758 758 1 0.0000000 16.0730000 5.3580000 10.7150000
|
||||
759 759 1 0.0000000 16.0730000 5.3580000 16.0730000
|
||||
760 760 1 0.0000000 16.0730000 5.3580000 21.4310000
|
||||
761 761 1 0.0000000 16.0730000 5.3580000 26.7880000
|
||||
762 762 1 0.0000000 16.0730000 5.3580000 32.1460000
|
||||
763 763 1 0.0000000 16.0730000 10.7150000 5.3580000
|
||||
764 764 1 0.0000000 16.0730000 10.7150000 10.7150000
|
||||
765 765 1 0.0000000 16.0730000 10.7150000 16.0730000
|
||||
766 766 1 0.0000000 16.0730000 10.7150000 21.4310000
|
||||
767 767 1 0.0000000 16.0730000 10.7150000 26.7880000
|
||||
768 768 1 0.0000000 16.0730000 10.7150000 32.1460000
|
||||
769 769 1 0.0000000 16.0730000 16.0730000 5.3580000
|
||||
770 770 1 0.0000000 16.0730000 16.0730000 10.7150000
|
||||
771 771 1 0.0000000 16.0730000 16.0730000 16.0730000
|
||||
772 772 1 0.0000000 16.0730000 16.0730000 21.4310000
|
||||
773 773 1 0.0000000 16.0730000 16.0730000 26.7880000
|
||||
774 774 1 0.0000000 16.0730000 16.0730000 32.1460000
|
||||
775 775 1 0.0000000 16.0730000 21.4310000 5.3580000
|
||||
776 776 1 0.0000000 16.0730000 21.4310000 10.7150000
|
||||
777 777 1 0.0000000 16.0730000 21.4310000 16.0730000
|
||||
778 778 1 0.0000000 16.0730000 21.4310000 21.4310000
|
||||
779 779 1 0.0000000 16.0730000 21.4310000 26.7880000
|
||||
780 780 1 0.0000000 16.0730000 21.4310000 32.1460000
|
||||
781 781 1 0.0000000 16.0730000 26.7880000 5.3580000
|
||||
782 782 1 0.0000000 16.0730000 26.7880000 10.7150000
|
||||
783 783 1 0.0000000 16.0730000 26.7880000 16.0730000
|
||||
784 784 1 0.0000000 16.0730000 26.7880000 21.4310000
|
||||
785 785 1 0.0000000 16.0730000 26.7880000 26.7880000
|
||||
786 786 1 0.0000000 16.0730000 26.7880000 32.1460000
|
||||
787 787 1 0.0000000 16.0730000 32.1460000 5.3580000
|
||||
788 788 1 0.0000000 16.0730000 32.1460000 10.7150000
|
||||
789 789 1 0.0000000 16.0730000 32.1460000 16.0730000
|
||||
790 790 1 0.0000000 16.0730000 32.1460000 21.4310000
|
||||
791 791 1 0.0000000 16.0730000 32.1460000 26.7880000
|
||||
792 792 1 0.0000000 16.0730000 32.1460000 32.1460000
|
||||
793 793 1 0.0000000 21.4310000 5.3580000 5.3580000
|
||||
794 794 1 0.0000000 21.4310000 5.3580000 10.7150000
|
||||
795 795 1 0.0000000 21.4310000 5.3580000 16.0730000
|
||||
796 796 1 0.0000000 21.4310000 5.3580000 21.4310000
|
||||
797 797 1 0.0000000 21.4310000 5.3580000 26.7880000
|
||||
798 798 1 0.0000000 21.4310000 5.3580000 32.1460000
|
||||
799 799 1 0.0000000 21.4310000 10.7150000 5.3580000
|
||||
800 800 1 0.0000000 21.4310000 10.7150000 10.7150000
|
||||
801 801 1 0.0000000 21.4310000 10.7150000 16.0730000
|
||||
802 802 1 0.0000000 21.4310000 10.7150000 21.4310000
|
||||
803 803 1 0.0000000 21.4310000 10.7150000 26.7880000
|
||||
804 804 1 0.0000000 21.4310000 10.7150000 32.1460000
|
||||
805 805 1 0.0000000 21.4310000 16.0730000 5.3580000
|
||||
806 806 1 0.0000000 21.4310000 16.0730000 10.7150000
|
||||
807 807 1 0.0000000 21.4310000 16.0730000 16.0730000
|
||||
808 808 1 0.0000000 21.4310000 16.0730000 21.4310000
|
||||
809 809 1 0.0000000 21.4310000 16.0730000 26.7880000
|
||||
810 810 1 0.0000000 21.4310000 16.0730000 32.1460000
|
||||
811 811 1 0.0000000 21.4310000 21.4310000 5.3580000
|
||||
812 812 1 0.0000000 21.4310000 21.4310000 10.7150000
|
||||
813 813 1 0.0000000 21.4310000 21.4310000 16.0730000
|
||||
814 814 1 0.0000000 21.4310000 21.4310000 21.4310000
|
||||
815 815 1 0.0000000 21.4310000 21.4310000 26.7880000
|
||||
816 816 1 0.0000000 21.4310000 21.4310000 32.1460000
|
||||
817 817 1 0.0000000 21.4310000 26.7880000 5.3580000
|
||||
818 818 1 0.0000000 21.4310000 26.7880000 10.7150000
|
||||
819 819 1 0.0000000 21.4310000 26.7880000 16.0730000
|
||||
820 820 1 0.0000000 21.4310000 26.7880000 21.4310000
|
||||
821 821 1 0.0000000 21.4310000 26.7880000 26.7880000
|
||||
822 822 1 0.0000000 21.4310000 26.7880000 32.1460000
|
||||
823 823 1 0.0000000 21.4310000 32.1460000 5.3580000
|
||||
824 824 1 0.0000000 21.4310000 32.1460000 10.7150000
|
||||
825 825 1 0.0000000 21.4310000 32.1460000 16.0730000
|
||||
826 826 1 0.0000000 21.4310000 32.1460000 21.4310000
|
||||
827 827 1 0.0000000 21.4310000 32.1460000 26.7880000
|
||||
828 828 1 0.0000000 21.4310000 32.1460000 32.1460000
|
||||
829 829 1 0.0000000 26.7880000 5.3580000 5.3580000
|
||||
830 830 1 0.0000000 26.7880000 5.3580000 10.7150000
|
||||
831 831 1 0.0000000 26.7880000 5.3580000 16.0730000
|
||||
832 832 1 0.0000000 26.7880000 5.3580000 21.4310000
|
||||
833 833 1 0.0000000 26.7880000 5.3580000 26.7880000
|
||||
834 834 1 0.0000000 26.7880000 5.3580000 32.1460000
|
||||
835 835 1 0.0000000 26.7880000 10.7150000 5.3580000
|
||||
836 836 1 0.0000000 26.7880000 10.7150000 10.7150000
|
||||
837 837 1 0.0000000 26.7880000 10.7150000 16.0730000
|
||||
838 838 1 0.0000000 26.7880000 10.7150000 21.4310000
|
||||
839 839 1 0.0000000 26.7880000 10.7150000 26.7880000
|
||||
840 840 1 0.0000000 26.7880000 10.7150000 32.1460000
|
||||
841 841 1 0.0000000 26.7880000 16.0730000 5.3580000
|
||||
842 842 1 0.0000000 26.7880000 16.0730000 10.7150000
|
||||
843 843 1 0.0000000 26.7880000 16.0730000 16.0730000
|
||||
844 844 1 0.0000000 26.7880000 16.0730000 21.4310000
|
||||
845 845 1 0.0000000 26.7880000 16.0730000 26.7880000
|
||||
846 846 1 0.0000000 26.7880000 16.0730000 32.1460000
|
||||
847 847 1 0.0000000 26.7880000 21.4310000 5.3580000
|
||||
848 848 1 0.0000000 26.7880000 21.4310000 10.7150000
|
||||
849 849 1 0.0000000 26.7880000 21.4310000 16.0730000
|
||||
850 850 1 0.0000000 26.7880000 21.4310000 21.4310000
|
||||
851 851 1 0.0000000 26.7880000 21.4310000 26.7880000
|
||||
852 852 1 0.0000000 26.7880000 21.4310000 32.1460000
|
||||
853 853 1 0.0000000 26.7880000 26.7880000 5.3580000
|
||||
854 854 1 0.0000000 26.7880000 26.7880000 10.7150000
|
||||
855 855 1 0.0000000 26.7880000 26.7880000 16.0730000
|
||||
856 856 1 0.0000000 26.7880000 26.7880000 21.4310000
|
||||
857 857 1 0.0000000 26.7880000 26.7880000 26.7880000
|
||||
858 858 1 0.0000000 26.7880000 26.7880000 32.1460000
|
||||
859 859 1 0.0000000 26.7880000 32.1460000 5.3580000
|
||||
860 860 1 0.0000000 26.7880000 32.1460000 10.7150000
|
||||
861 861 1 0.0000000 26.7880000 32.1460000 16.0730000
|
||||
862 862 1 0.0000000 26.7880000 32.1460000 21.4310000
|
||||
863 863 1 0.0000000 26.7880000 32.1460000 26.7880000
|
||||
864 864 1 0.0000000 26.7880000 32.1460000 32.1460000
|
||||
|
||||
|
|
@ -0,0 +1,20 @@
|
|||
#############################
|
||||
#Atoms types - mass - charge#
|
||||
#############################
|
||||
#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
|
||||
|
||||
variable Ar equal 1
|
||||
|
||||
#############
|
||||
#Atom Masses#
|
||||
#############
|
||||
|
||||
mass ${Ar} 39.903
|
||||
|
||||
###########################
|
||||
#Pair Potentials - Tersoff#
|
||||
###########################
|
||||
|
||||
pair_style lj/cubic
|
||||
pair_coeff * * 0.0102701 3.42
|
||||
|
||||
|
|
@ -0,0 +1,162 @@
|
|||
###############################mm
|
||||
# Atom style - charge/vdw/bonded#
|
||||
#################################
|
||||
atom_style full
|
||||
|
||||
##############################################
|
||||
#Units Metal : eV - ps - angstrom - bar#
|
||||
# Real : kcal/mol - fs - angstrom - atm#
|
||||
##############################################
|
||||
units metal
|
||||
|
||||
############
|
||||
#Run number#
|
||||
############
|
||||
variable run_no equal 0 # is it a restart?
|
||||
variable res_no equal ${run_no}-1 # restart file number
|
||||
|
||||
#######################################
|
||||
#Random Seeds and Domain Decomposition#
|
||||
#######################################
|
||||
variable iseed0 equal 2357
|
||||
variable iseed1 equal 26488
|
||||
variable iseed2 equal 10669
|
||||
processors * * *
|
||||
|
||||
###########
|
||||
#Data File#
|
||||
###########
|
||||
variable inpfile string argon.lmp
|
||||
variable resfile string final_restart.${res_no}
|
||||
variable ff_file string ff-argon.lmp
|
||||
|
||||
##########
|
||||
#Run Type#
|
||||
##########
|
||||
variable minimise equal 0 #Energy Minimization
|
||||
variable md equal 1 #Plain MD
|
||||
|
||||
###############################
|
||||
#Molecular Dynamics Parameters#
|
||||
###############################
|
||||
variable run_no equal 0 # is it a restart?
|
||||
|
||||
variable ens equal 9 # ensemble (0=nve, 1=nvt, 2=npt, 3=ber, 4=lang, 5=stoc, 6=vres, 7=stoch, 8=gjf)
|
||||
variable ts equal 0.120 # simulation timestep (time units)
|
||||
variable nequil equal 0 # number of equilibration steps
|
||||
variable nsteps equal 200000 # number of MD steps
|
||||
#variable nsteps equal 20 # number of MD steps
|
||||
|
||||
variable temp_s equal 10 # starting temperature
|
||||
variable temp_f equal 10 # final simulation temperature
|
||||
variable trel equal 1 # thermostat relaxation time
|
||||
variable tscale equal 1 # thermostat relaxation freq - vel rescaling only
|
||||
variable deltat equal 1 # maximum temperature change - vel rescaling only
|
||||
|
||||
variable npttype string iso # type of NPT (iso, aniso, tri, z...)
|
||||
variable pres equal 1.01325 # pressure (NPT runs only)
|
||||
variable prel equal 1.0 # barostat relaxation time
|
||||
|
||||
neighbor 1 bin
|
||||
|
||||
###################
|
||||
#Output Parameters#
|
||||
###################
|
||||
variable ntraj equal 1000 # trajectory output frequency - all system
|
||||
variable ntraj_s equal -100 # trajectory output frequency - solute only
|
||||
variable nthermo equal 200 # thermodynamic data output frequency
|
||||
|
||||
################################
|
||||
#Energy Minimization Parameters#
|
||||
################################
|
||||
variable mtraj equal 1 # trajectory output frequency - all system
|
||||
variable etol equal 1e-5 # % change in energy
|
||||
variable ftol equal 1e-5 # max force threshold (force units)
|
||||
variable maxiter equal 10000 # max # of iterations
|
||||
|
||||
########################
|
||||
#3D Periodic Simulation#
|
||||
########################
|
||||
boundary p p p
|
||||
|
||||
#############################
|
||||
#Reading the input structure#
|
||||
#############################
|
||||
if "${run_no} == 0" then "read_data ${inpfile}" else "read_restart ${resfile}"
|
||||
|
||||
#############
|
||||
#Force Field#
|
||||
#############
|
||||
include ${ff_file}
|
||||
|
||||
######################
|
||||
#Thermodynamic Output#
|
||||
######################
|
||||
variable str_basic string 'step time pe temp press'
|
||||
|
||||
#MD ensemble (0=nve, 1=nvt, 2=npt, 3=ber, 4=lang, 5=stoc, 6=vres)
|
||||
variable str_ens string ' '
|
||||
if "${ens} == 0" then "variable str_ens string 'etotal'"
|
||||
if "${ens} == 2" then "variable str_ens string 'vol pxx pyy pzz cella cellb cellc cellakpha cellbeta cellgamma'"
|
||||
|
||||
#Variable for a gulp friend output
|
||||
if "${ens} >= 0" then "thermo_style custom time temp pe etotal press vol cpu" &
|
||||
"thermo ${nthermo}" &
|
||||
"thermo_modify flush yes"
|
||||
|
||||
#####################
|
||||
#Energy Minimization#
|
||||
#####################
|
||||
if "${minimise} <= 0 || ${run_no} > 0" then "jump SELF end_minimise"
|
||||
print "Doing CG minimisation"
|
||||
dump mdcd all dcd ${mtraj} min.dcd
|
||||
dump_modify mdcd unwrap yes
|
||||
min_style cg
|
||||
min_modify line quadratic
|
||||
minimize ${etol} ${ftol} ${maxiter} ${maxiter}
|
||||
reset_timestep 0
|
||||
undump mdcd
|
||||
label end_minimise
|
||||
|
||||
################
|
||||
#Timestep in ps#
|
||||
################
|
||||
timestep ${ts}
|
||||
|
||||
##############
|
||||
#Restart file#
|
||||
##############
|
||||
restart 100000 restart.1 restart.2
|
||||
|
||||
###################
|
||||
#Trajectory output#
|
||||
###################
|
||||
#dump xyz all atom 1000 silicon.lammpstrj
|
||||
|
||||
if "${ntraj} > 0" then &
|
||||
"dump 1 all dcd ${ntraj} trajectory.${run_no}.dcd" &
|
||||
"dump_modify 1 unwrap yes"
|
||||
|
||||
fix mom all momentum 1 linear 1 1 1
|
||||
|
||||
###############################################################
|
||||
#Ensembles (0=nve,1=nvt, 2=npt, 3=ber, 4=lang, 5=stoc, 6=vres)#
|
||||
###############################################################
|
||||
if "${md} > 0" then 'print "Setting up the ensembles"' &
|
||||
'if "${run_no} == 0" then "velocity all create ${temp_s} ${iseed0} mom yes dist gaussian"' &
|
||||
'if "${ens} == 0" then "fix nve all nve"' &
|
||||
'if "${ens} == 1" then "fix nvt all nvt temp ${temp_s} ${temp_f} ${trel} tchain 5"' &
|
||||
'if "${ens} == 2" then "fix npt all npt temp ${temp_s} ${temp_f} ${trel} ${npttype} ${pres} ${pres} ${prel} tchain 5 pchain 5 mtk yes"' &
|
||||
'if "${ens} == 3" then "fix nve all nve" "fix ber all temp/berendsen ${temp_s} ${temp_f} ${trel}"' &
|
||||
'if "${ens} == 4" then "fix nve all nve" "fix lang all langevin ${temp_s} ${temp_f} ${trel} ${iseed1} tally yes zero yes"' &
|
||||
'if "${ens} == 5" then "fix nve all nve" "fix stoch all temp/csvr ${temp_s} ${temp_f} ${trel} ${iseed1}"' &
|
||||
'if "${ens} == 6" then "fix nve all nve" "fix stoch all temp/csld ${temp_s} ${temp_f} ${trel} ${iseed1}"' &
|
||||
'if "${ens} == 7" then "fix nve all nve" "fix vres all temp/rescale ${tscale} ${temp_s} ${temp_f} ${tmin} ${tmax}"' &
|
||||
'if "${ens} == 8" then "fix nve all nve" "fix lang all langevin ${temp_s} ${temp_f} ${trel} ${iseed1} gjf yes"' &
|
||||
'if "${ens} == 9" then "fix nve all nve" "fix lang all langevin ${temp_s} ${temp_f} ${trel} ${iseed1} gjf yes halfstep yes"'
|
||||
|
||||
if "${md} > 0" then "print 'Doing Molecular dynamics'" &
|
||||
"run ${nsteps}" &
|
||||
"write_restart final_restart.${run_no}"
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,249 @@
|
|||
LAMMPS (1 Feb 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (32.146 32.146 32.146)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
864 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
Setting up the ensembles
|
||||
WARNING: Careful, tally is untested (src/fix_langevin.cpp:145)
|
||||
WARNING: Careful, tally is untested (src/fix_langevin.cpp:145)
|
||||
WARNING: Careful, tally is untested (src/fix_langevin.cpp:145)
|
||||
WARNING: Careful, tally is untested (src/fix_langevin.cpp:145)
|
||||
Doing Molecular dynamics
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.94072
|
||||
ghost atom cutoff = 6.94072
|
||||
binsize = 3.47036, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cubic, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : metal
|
||||
Current step : 0
|
||||
Time step : 0.12
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.847 | 6.847 | 6.847 Mbytes
|
||||
Time Temp PotEng TotEng Press Volume CPU
|
||||
0 10 -56.207655 -55.09214 33.340921 33218.561 0
|
||||
24 10.156356 -55.092888 -53.959932 339.40964 33218.561 0.082175482
|
||||
48 9.6121006 -55.07262 -54.000376 344.56765 33218.561 0.19529325
|
||||
72 9.8187467 -55.16687 -54.071574 318.85979 33218.561 0.29643488
|
||||
96 9.5421385 -55.151229 -54.086789 322.8842 33218.561 0.38801357
|
||||
120 10.295035 -55.12919 -53.980763 332.00171 33218.561 0.47607262
|
||||
144 10.331608 -55.09907 -53.946563 339.28896 33218.561 0.57389224
|
||||
168 10.154698 -55.058246 -53.925475 349.03253 33218.561 0.65481471
|
||||
192 9.858198 -55.127583 -54.027886 330.09298 33218.561 0.74437734
|
||||
216 9.6658918 -55.10812 -54.029875 334.28383 33218.561 0.8278495
|
||||
240 9.6801591 -55.102386 -54.02255 336.27242 33218.561 0.91167379
|
||||
264 10.685658 -55.046238 -53.854237 355.0448 33218.561 1.0023789
|
||||
288 10.387727 -55.08427 -53.925504 343.87247 33218.561 1.0960371
|
||||
312 10.231132 -55.120428 -53.97913 333.22463 33218.561 1.2382998
|
||||
336 10.20896 -55.075142 -53.936317 344.88438 33218.561 1.3420489
|
||||
360 9.7876538 -55.165008 -54.07318 319.14962 33218.561 1.42782
|
||||
384 9.9872551 -55.13881 -54.024717 327.82471 33218.561 1.5417666
|
||||
408 9.5362734 -55.063733 -53.999947 346.50545 33218.561 1.6328366
|
||||
432 10.262638 -55.126608 -53.981796 332.16342 33218.561 1.7242996
|
||||
456 9.9228239 -55.122119 -54.015214 332.26261 33218.561 1.8124888
|
||||
480 9.7026324 -55.17057 -54.088227 317.84818 33218.561 1.900233
|
||||
504 10.028762 -55.082465 -53.963741 343.04257 33218.561 1.989605
|
||||
528 9.8227851 -55.121222 -54.025476 332.42857 33218.561 2.0708802
|
||||
552 10.208672 -55.100242 -53.961449 338.68109 33218.561 2.1527217
|
||||
576 10.180849 -55.124065 -53.988376 331.29516 33218.561 2.238126
|
||||
600 9.6467252 -55.119533 -54.043427 332.43109 33218.561 2.323443
|
||||
624 10.041885 -55.173802 -54.053614 318.48579 33218.561 2.4046151
|
||||
648 10.151597 -55.111725 -53.979299 334.66227 33218.561 2.4902161
|
||||
672 9.7719111 -55.060111 -53.970039 348.55249 33218.561 2.5800372
|
||||
696 10.476688 -55.088109 -53.919419 342.94922 33218.561 2.6731395
|
||||
720 10.517805 -55.113604 -53.940327 335.47342 33218.561 2.760651
|
||||
744 10.006466 -55.045085 -53.928848 353.53813 33218.561 2.8537894
|
||||
768 10.201492 -55.081598 -53.943606 343.3206 33218.561 2.9404115
|
||||
792 10.117738 -55.077806 -53.949157 345.31093 33218.561 3.030765
|
||||
816 10.362288 -55.11635 -53.960421 333.9045 33218.561 3.1177356
|
||||
840 10.204164 -55.097619 -53.959329 338.82717 33218.561 3.2091886
|
||||
864 10.147722 -55.101372 -53.969378 338.19682 33218.561 3.3003742
|
||||
888 9.9265037 -55.111394 -54.004077 334.08116 33218.561 3.395341
|
||||
912 10.206403 -55.132181 -53.993642 328.89904 33218.561 3.4882881
|
||||
936 10.28639 -55.093317 -53.945855 340.61244 33218.561 3.5764735
|
||||
960 9.8028822 -55.078802 -53.985276 343.5904 33218.561 3.7056267
|
||||
984 10.492755 -55.121321 -53.950839 334.62697 33218.561 3.8055611
|
||||
1008 10.621569 -55.088588 -53.903736 343.33166 33218.561 3.9144807
|
||||
1032 10.006729 -55.113459 -53.997193 334.43025 33218.561 4.0189888
|
||||
1056 10.099853 -55.068035 -53.941381 347.42158 33218.561 4.1391664
|
||||
1080 10.254232 -55.066685 -53.92281 347.15777 33218.561 4.2443953
|
||||
1104 9.9495142 -55.13686 -54.026977 327.63107 33218.561 4.3368342
|
||||
1128 10.377108 -55.08846 -53.930878 344.13083 33218.561 4.4287748
|
||||
1152 10.036981 -55.114643 -53.995003 334.88053 33218.561 4.526868
|
||||
1176 10.144779 -55.097125 -53.965459 339.698 33218.561 4.6614049
|
||||
1200 10.075844 -55.14695 -54.022974 326.05911 33218.561 4.799835
|
||||
1224 10.183695 -55.121716 -53.98571 332.75772 33218.561 4.8908897
|
||||
1248 10.581369 -55.027954 -53.847587 359.06251 33218.561 4.9839788
|
||||
1272 10.158269 -55.105173 -53.972003 337.52964 33218.561 5.0918646
|
||||
1296 9.8776072 -55.064085 -53.962223 347.15648 33218.561 5.2291209
|
||||
1320 10.38161 -55.118366 -53.960282 335.17767 33218.561 5.3570446
|
||||
1344 9.9528146 -55.141937 -54.031685 326.27117 33218.561 5.4584705
|
||||
1368 9.8024326 -55.117808 -54.024332 332.99835 33218.561 5.5557818
|
||||
1392 10.35447 -55.110235 -53.955179 336.80412 33218.561 5.6467392
|
||||
1416 10.199061 -55.105641 -53.96792 337.36785 33218.561 5.7476527
|
||||
1440 9.6868779 -55.087316 -54.00673 340.9166 33218.561 5.8432207
|
||||
1464 10.093238 -55.049436 -53.92352 352.27563 33218.561 5.9471521
|
||||
1488 9.7578808 -55.123935 -54.035429 329.93926 33218.561 6.0495014
|
||||
1512 10.099979 -55.205426 -54.078758 309.26166 33218.561 6.1612976
|
||||
1536 10.172944 -55.087106 -53.952299 342.93395 33218.561 6.2506202
|
||||
1560 10.51771 -55.107635 -53.934369 340.1967 33218.561 6.3379856
|
||||
1584 10.044994 -55.101362 -53.980828 339.03163 33218.561 6.4362567
|
||||
1608 9.624758 -55.146246 -54.07259 324.32486 33218.561 6.5385845
|
||||
1632 9.9135215 -55.097278 -53.99141 338.69162 33218.561 6.6452786
|
||||
1656 9.863681 -55.070523 -53.970214 345.84608 33218.561 6.7518212
|
||||
1680 10.138513 -55.127065 -53.996099 330.40757 33218.561 6.8775188
|
||||
1704 10.382237 -55.070572 -53.912417 347.074 33218.561 7.0126448
|
||||
1728 10.72487 -55.081147 -53.884771 345.83623 33218.561 7.1384216
|
||||
1752 9.829431 -55.131041 -54.034553 328.57652 33218.561 7.2616419
|
||||
1776 9.9135662 -55.100556 -53.994682 336.52238 33218.561 7.4193201
|
||||
1800 10.41873 -55.097116 -53.934891 340.24798 33218.561 7.5570544
|
||||
1824 10.151782 -55.03231 -53.899864 357.3654 33218.561 7.6872905
|
||||
1848 10.42307 -55.043808 -53.881099 355.71677 33218.561 7.7933885
|
||||
1872 10.276862 -55.085016 -53.938616 344.46273 33218.561 7.8887472
|
||||
1896 9.7681373 -55.146507 -54.056857 324.84323 33218.561 7.9977923
|
||||
1920 9.6624824 -55.103214 -54.025349 336.06397 33218.561 8.090235
|
||||
1944 10.153504 -55.049175 -53.916536 352.36339 33218.561 8.1923703
|
||||
1968 10.191954 -55.098741 -53.961813 338.8667 33218.561 8.3320906
|
||||
1992 9.92167 -55.117079 -54.010302 332.96497 33218.561 8.4774437
|
||||
2016 9.5737281 -55.091141 -54.023178 339.41837 33218.561 8.6149527
|
||||
2040 10.600908 -55.092717 -53.91017 342.71852 33218.561 8.7639523
|
||||
2064 9.9214513 -55.099904 -53.993151 337.46799 33218.561 8.898087
|
||||
2088 9.9256258 -55.082224 -53.975005 342.85042 33218.561 9.0130784
|
||||
2112 10.345379 -55.112923 -53.95888 335.81471 33218.561 9.1422766
|
||||
2136 9.8876649 -55.079254 -53.97627 343.05764 33218.561 9.2885707
|
||||
2160 10.04492 -55.074876 -53.95435 344.82419 33218.561 9.3876103
|
||||
2184 10.028705 -55.063961 -53.945244 347.70549 33218.561 9.500967
|
||||
2208 10.412572 -55.136316 -53.974778 329.8188 33218.561 9.5900362
|
||||
2232 10.404205 -55.09913 -53.938525 339.77542 33218.561 9.7048353
|
||||
2256 9.5694135 -55.139021 -54.071538 326.37473 33218.561 9.8045958
|
||||
2280 10.244745 -55.134529 -53.991713 329.19392 33218.561 9.8968908
|
||||
2304 9.9129922 -55.116192 -54.010382 333.14326 33218.561 9.9818651
|
||||
2328 10.167027 -55.08241 -53.948263 343.08135 33218.561 10.068683
|
||||
2352 10.262045 -55.144327 -53.999581 327.40876 33218.561 10.155937
|
||||
2376 10.520934 -55.073147 -53.899521 347.6998 33218.561 10.246316
|
||||
2400 9.9628692 -55.122001 -54.010628 331.25369 33218.561 10.336833
|
||||
2424 10.565531 -55.157113 -53.978512 325.14897 33218.561 10.452039
|
||||
2448 10.03709 -55.096409 -53.976756 338.29607 33218.561 10.537936
|
||||
2472 9.384311 -55.141821 -54.094987 324.23247 33218.561 10.628689
|
||||
2496 9.8019362 -55.105685 -54.012264 335.97239 33218.561 10.717287
|
||||
2520 10.31114 -55.078831 -53.928608 345.42395 33218.561 10.818756
|
||||
2544 10.407237 -55.148382 -53.987439 325.94421 33218.561 10.910801
|
||||
2568 10.257967 -55.041348 -53.897056 355.73261 33218.561 11.004221
|
||||
2592 9.8425807 -55.139428 -54.041474 328.28096 33218.561 11.101295
|
||||
2616 10.140697 -55.100238 -53.969028 338.76319 33218.561 11.192211
|
||||
2640 9.7102818 -55.136288 -54.053091 326.7053 33218.561 11.280277
|
||||
2664 10.120372 -55.128779 -53.999836 330.71707 33218.561 11.369001
|
||||
2688 10.232537 -55.120614 -53.979159 333.35087 33218.561 11.464652
|
||||
2712 10.032526 -55.094761 -53.975618 339.97984 33218.561 11.559387
|
||||
2736 9.8791 -55.121998 -54.01997 332.32556 33218.561 11.649679
|
||||
2760 9.891483 -55.120919 -54.017509 331.32614 33218.561 11.742604
|
||||
2784 10.201053 -55.165525 -54.027582 320.39272 33218.561 11.85274
|
||||
2808 10.238648 -55.096449 -53.954312 340.06316 33218.561 11.939782
|
||||
2832 9.8692851 -55.068632 -53.967699 346.77535 33218.561 12.036655
|
||||
2856 10.179976 -55.128413 -53.992822 331.5662 33218.561 12.123227
|
||||
2880 9.7656315 -55.1468 -54.057429 324.02612 33218.561 12.213117
|
||||
2904 9.7991628 -55.049191 -53.95608 352.45738 33218.561 12.326761
|
||||
2928 10.581767 -55.093293 -53.912881 341.37292 33218.561 12.417633
|
||||
2952 10.546144 -55.07452 -53.898081 347.02025 33218.561 12.52701
|
||||
2976 9.8306008 -55.14762 -54.051002 323.45715 33218.561 12.633522
|
||||
3000 10.033532 -55.076433 -53.957178 345.36812 33218.561 12.72627
|
||||
3024 10.046266 -55.085775 -53.965099 342.47786 33218.561 12.816242
|
||||
3048 10.176777 -55.133013 -53.997778 329.04144 33218.561 12.903175
|
||||
3072 9.9778064 -55.143787 -54.030748 326.75284 33218.561 13.014329
|
||||
3096 10.516223 -55.110144 -53.937043 336.802 33218.561 13.104673
|
||||
3120 9.6561157 -55.138699 -54.061544 325.6652 33218.561 13.207371
|
||||
3144 10.237043 -55.060968 -53.91901 349.44011 33218.561 13.303442
|
||||
3168 9.9704264 -55.123073 -54.010857 332.19725 33218.561 13.391877
|
||||
3192 10.493307 -55.144402 -53.973858 327.15485 33218.561 13.482857
|
||||
3216 10.022171 -55.141782 -54.023794 326.08249 33218.561 13.574484
|
||||
3240 9.6957248 -55.137865 -54.056292 326.04858 33218.561 13.671408
|
||||
3264 9.9685299 -55.124301 -54.012297 331.9015 33218.561 13.760186
|
||||
3288 10.413707 -55.153604 -53.99194 324.32939 33218.561 13.877604
|
||||
3312 10.022953 -55.103422 -53.985346 337.52066 33218.561 13.977562
|
||||
3336 10.044478 -55.110297 -53.98982 334.48379 33218.561 14.065563
|
||||
3360 9.8593734 -55.130623 -54.030795 327.71748 33218.561 14.15952
|
||||
3384 9.9269422 -55.107979 -54.000613 335.18173 33218.561 14.258064
|
||||
3408 10.288049 -55.092276 -53.944629 340.71484 33218.561 14.36211
|
||||
3432 9.9702156 -55.08732 -53.975128 341.72171 33218.561 14.452123
|
||||
3456 10.246178 -55.091669 -53.948692 341.62844 33218.561 14.555775
|
||||
3480 10.559292 -55.086917 -53.909012 343.70626 33218.561 14.645718
|
||||
3504 10.652207 -55.050897 -53.862628 354.46979 33218.561 14.797422
|
||||
3528 9.9835266 -55.0557 -53.942023 350.74747 33218.561 14.895716
|
||||
3552 10.240934 -55.123217 -53.980825 332.26434 33218.561 15.023796
|
||||
3576 10.406519 -55.093536 -53.932674 341.54029 33218.561 15.203252
|
||||
3600 10.406733 -55.095168 -53.934282 341.22192 33218.561 15.303986
|
||||
3624 9.9877484 -55.154231 -54.040083 323.55633 33218.561 15.398883
|
||||
3648 10.391829 -55.110208 -53.950984 337.09219 33218.561 15.49042
|
||||
3672 10.368995 -55.069591 -53.912914 346.82649 33218.561 15.582259
|
||||
3696 10.362939 -55.109012 -53.953011 337.32216 33218.561 15.679316
|
||||
3720 10.465254 -55.136214 -53.968799 331.22288 33218.561 15.773303
|
||||
3744 9.8238226 -55.10114 -54.005278 338.12616 33218.561 15.86905
|
||||
3768 10.205504 -55.101263 -53.962824 339.04196 33218.561 15.960072
|
||||
3792 9.9589987 -55.118883 -54.007942 332.84318 33218.561 16.047055
|
||||
3816 10.253382 -55.117513 -53.973732 334.42101 33218.561 16.148412
|
||||
3840 10.262393 -55.069549 -53.924764 349.084 33218.561 16.235391
|
||||
3864 9.7367167 -55.078288 -53.992142 342.48207 33218.561 16.329112
|
||||
3888 10.171202 -55.134701 -54.000088 329.5847 33218.561 16.415353
|
||||
3912 10.01925 -55.145139 -54.027477 326.65074 33218.561 16.526334
|
||||
3936 10.053638 -55.038151 -53.916653 355.74893 33218.561 16.618524
|
||||
3960 10.044055 -55.058382 -53.937953 349.01834 33218.561 16.712577
|
||||
3984 10.382422 -55.099216 -53.941041 339.28099 33218.561 16.79941
|
||||
4008 9.97927 -55.09284 -53.979637 339.07225 33218.561 16.904198
|
||||
4032 9.6782319 -55.126143 -54.046522 329.0201 33218.561 16.991454
|
||||
4056 9.6593809 -55.123677 -54.046159 329.89833 33218.561 17.097172
|
||||
4080 10.442896 -55.141149 -53.976229 327.9899 33218.561 17.189364
|
||||
4104 9.9571109 -55.08588 -53.975149 341.3746 33218.561 17.294147
|
||||
4128 10.44943 -55.087946 -53.922296 343.09435 33218.561 17.387357
|
||||
4152 10.040581 -55.171939 -54.051897 317.85348 33218.561 17.500905
|
||||
4176 10.089442 -55.128713 -54.00322 330.29121 33218.561 17.588891
|
||||
4200 10.316156 -55.123219 -53.972436 333.59382 33218.561 17.679254
|
||||
4224 10.177245 -55.095671 -53.960384 339.34498 33218.561 17.770569
|
||||
4248 9.7129183 -55.135335 -54.051844 328.25125 33218.561 17.857728
|
||||
4272 10.231838 -55.099554 -53.958177 339.64015 33218.561 17.944226
|
||||
4296 9.9737677 -55.117885 -54.005297 333.07248 33218.561 18.034105
|
||||
4320 10.004955 -55.116155 -54.000088 333.52271 33218.561 18.129644
|
||||
4344 9.5938901 -55.133824 -54.063612 327.84171 33218.561 18.215476
|
||||
4368 9.8954562 -55.131603 -54.02775 329.0813 33218.561 18.306539
|
||||
4392 10.439732 -55.100379 -53.935812 339.81679 33218.561 18.395651
|
||||
4416 9.934513 -55.08449 -53.97628 341.74441 33218.561 18.484506
|
||||
4440 10.025998 -55.136771 -54.018356 327.73718 33218.561 18.593946
|
||||
4464 9.9304451 -55.101817 -53.994061 338.1801 33218.561 18.684011
|
||||
4488 10.344371 -55.085856 -53.931926 342.91721 33218.561 18.782399
|
||||
4512 10.033193 -55.091778 -53.972561 339.85728 33218.561 18.879666
|
||||
4536 9.2361614 -55.169375 -54.139067 316.67597 33218.561 18.983667
|
||||
4560 9.5786289 -55.179976 -54.111465 314.76415 33218.561 19.079009
|
||||
4584 10.071651 -55.107218 -53.98371 336.10364 33218.561 19.163975
|
||||
4608 9.9873098 -55.109348 -53.995249 336.03665 33218.561 19.25635
|
||||
4632 10.143888 -55.119423 -53.987857 333.74978 33218.561 19.346658
|
||||
4656 9.7506264 -55.114772 -54.027075 332.98271 33218.561 19.435425
|
||||
4680 9.9616769 -55.096054 -53.984814 339.20499 33218.561 19.55562
|
||||
4704 10.271313 -55.074522 -53.928742 345.87397 33218.561 19.642652
|
||||
4728 9.9172336 -55.098805 -53.992523 338.06318 33218.561 19.734557
|
||||
4752 9.9556222 -55.12128 -54.010716 332.66408 33218.561 19.83859
|
||||
4776 10.197593 -55.095293 -53.957736 339.50067 33218.561 19.947471
|
||||
4800 10.145085 -55.108467 -53.976768 336.05115 33218.561 20.044183
|
||||
4824 10.205523 -55.147376 -54.008934 325.56559 33218.561 20.144393
|
||||
4848 9.8900281 -55.121598 -54.01835 331.17401 33218.561 20.243197
|
||||
4872 10.03655 -55.100936 -53.981343 337.6777 33218.561 20.336043
|
||||
4896 9.8120635 -55.087507 -53.992957 341.42438 33218.561 20.425498
|
||||
4920 10.615354 -55.093335 -53.909176 342.30776 33218.561 20.519318
|
||||
4944 10.374366 -55.06455 -53.907274 351.10607 33218.561 20.612312
|
||||
4968 10.677474 -55.147807 -53.956718 327.85703 33218.561 20.719371
|
||||
4992 10.558882 -55.145253 -53.967393 327.427 33218.561 20.818726
|
||||
5016 9.4097946 -55.150835 -54.101158 321.62641 33218.561 20.914472
|
||||
Binary file not shown.
|
|
@ -98,6 +98,7 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
|
|||
oflag = 0;
|
||||
tallyflag = 0;
|
||||
zeroflag = 0;
|
||||
hsflag = 0;
|
||||
|
||||
int iarg = 7;
|
||||
while (iarg < narg) {
|
||||
|
|
@ -138,6 +139,14 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
|
|||
else if (strcmp(arg[iarg+1],"yes") == 0) zeroflag = 1;
|
||||
else error->all(FLERR,"Illegal fix langevin command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"halfstep") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix langevin command");
|
||||
if (gjfflag == 0) error->all(FLERR,"GJF must be set");
|
||||
if (tallyflag == 0) error->warning(FLERR,"Careful, tally is untested");
|
||||
if (strcmp(arg[iarg+1],"no") == 0) hsflag = 0;
|
||||
else if (strcmp(arg[iarg+1],"yes") == 0) hsflag = 1;
|
||||
else error->all(FLERR,"Illegal fix langevin command");
|
||||
iarg += 2;
|
||||
} else error->all(FLERR,"Illegal fix langevin command");
|
||||
}
|
||||
|
||||
|
|
@ -155,6 +164,8 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
|
|||
flangevin = NULL;
|
||||
flangevin_allocated = 0;
|
||||
franprev = NULL;
|
||||
wildcard = NULL;
|
||||
lv = NULL;
|
||||
tforce = NULL;
|
||||
maxatom1 = maxatom2 = 0;
|
||||
|
||||
|
|
@ -163,6 +174,12 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
|
|||
// no need to set peratom_flag, b/c data is for internal use only
|
||||
|
||||
if (gjfflag) {
|
||||
int mem = 6*atom->nmax*sizeof(double);
|
||||
if (hsflag) mem += 3*atom->nmax*sizeof(double);
|
||||
|
||||
comm->maxexchange_fix = MAX(comm->maxexchange_fix, 0);
|
||||
comm->maxexchange_fix += MAX(1000, mem);
|
||||
|
||||
nvalues = 3;
|
||||
grow_arrays(atom->nmax);
|
||||
atom->add_callback(0);
|
||||
|
|
@ -174,6 +191,14 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
|
|||
franprev[i][0] = 0.0;
|
||||
franprev[i][1] = 0.0;
|
||||
franprev[i][2] = 0.0;
|
||||
wildcard[i][0] = 0.0;
|
||||
wildcard[i][1] = 0.0;
|
||||
wildcard[i][2] = 0.0;
|
||||
if (hsflag) {
|
||||
lv[i][0] = 0.0;
|
||||
lv[i][1] = 0.0;
|
||||
lv[i][2] = 0.0;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -194,6 +219,8 @@ FixLangevin::~FixLangevin()
|
|||
|
||||
if (gjfflag) {
|
||||
memory->destroy(franprev);
|
||||
memory->destroy(wildcard);
|
||||
if (hsflag) memory->destroy(lv);
|
||||
atom->delete_callback(id,0);
|
||||
}
|
||||
}
|
||||
|
|
@ -203,6 +230,8 @@ FixLangevin::~FixLangevin()
|
|||
int FixLangevin::setmask()
|
||||
{
|
||||
int mask = 0;
|
||||
//if (gjfflag) mask |= INITIAL_INTEGRATE;
|
||||
if (gjfflag) mask |= POST_INTEGRATE;
|
||||
mask |= POST_FORCE;
|
||||
mask |= POST_FORCE_RESPA;
|
||||
mask |= END_OF_STEP;
|
||||
|
|
@ -258,13 +287,11 @@ void FixLangevin::init()
|
|||
error->one(FLERR,"Fix langevin angmom requires extended particles");
|
||||
}
|
||||
|
||||
// set force prefactors
|
||||
|
||||
if (!atom->rmass) {
|
||||
for (int i = 1; i <= atom->ntypes; i++) {
|
||||
gfactor1[i] = -atom->mass[i] / t_period / force->ftm2v;
|
||||
gfactor2[i] = sqrt(atom->mass[i]) *
|
||||
sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) /
|
||||
sqrt(2.0*force->boltz/t_period/update->dt/force->mvv2e) /
|
||||
force->ftm2v;
|
||||
gfactor1[i] *= 1.0/ratio[i];
|
||||
gfactor2[i] *= 1.0/sqrt(ratio[i]);
|
||||
|
|
@ -277,7 +304,7 @@ void FixLangevin::init()
|
|||
if (strstr(update->integrate_style,"respa"))
|
||||
nlevels_respa = ((Respa *) update->integrate)->nlevels;
|
||||
|
||||
if (gjfflag) gjffac = 1.0/(1.0+update->dt/2.0/t_period);
|
||||
if (gjfflag) gjffac = 1.0/sqrt(1.0+update->dt/2.0/t_period);
|
||||
|
||||
}
|
||||
|
||||
|
|
@ -292,6 +319,94 @@ void FixLangevin::setup(int vflag)
|
|||
post_force_respa(vflag,nlevels_respa-1,0);
|
||||
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
|
||||
}
|
||||
if (gjfflag && hsflag) {
|
||||
|
||||
double dt = update->dt;
|
||||
|
||||
// update v of atoms in group
|
||||
|
||||
double **v = atom->v;
|
||||
double *rmass = atom->rmass;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||
|
||||
double boltz = force->boltz;
|
||||
double mvv2e = force->mvv2e;
|
||||
double ftm2v = force->ftm2v;
|
||||
|
||||
double gamma2;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (rmass) {
|
||||
gamma2 = sqrt(rmass[i]) * sqrt(2.0*boltz/t_period/dt/mvv2e) / ftm2v;
|
||||
gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
|
||||
} else {
|
||||
gamma2 = gfactor2[type[i]] * tsqrt;
|
||||
}
|
||||
|
||||
franprev[i][0] = gamma2*random->gaussian();
|
||||
franprev[i][1] = gamma2*random->gaussian();
|
||||
franprev[i][2] = gamma2*random->gaussian();
|
||||
wildcard[i][0] = v[i][0];
|
||||
wildcard[i][1] = v[i][1];
|
||||
wildcard[i][2] = v[i][2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allow for both per-type and per-atom mass
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixLangevin::post_integrate()
|
||||
{
|
||||
double dtfm;
|
||||
double dt = update->dt;
|
||||
double dtf = 0.5 * dt * force->ftm2v;
|
||||
|
||||
// update v of atoms in group
|
||||
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
double *rmass = atom->rmass;
|
||||
double *mass = atom->mass;
|
||||
int *type = atom->type;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||
|
||||
if (rmass) {
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
dtfm = dtf / rmass[i];
|
||||
x[i][0] += -dt * v[i][0];
|
||||
x[i][1] += -dt * v[i][1];
|
||||
x[i][2] += -dt * v[i][2];
|
||||
v[i][0] = gjffac * (wildcard[i][0] + dtfm * franprev[i][0] + dtfm * f[i][0]);
|
||||
v[i][1] = gjffac * (wildcard[i][1] + dtfm * franprev[i][1] + dtfm * f[i][1]);
|
||||
v[i][2] = gjffac * (wildcard[i][2] + dtfm * franprev[i][2] + dtfm * f[i][2]);
|
||||
x[i][0] += gjffac * dt * v[i][0];
|
||||
x[i][1] += gjffac * dt * v[i][1];
|
||||
x[i][2] += gjffac * dt * v[i][2];
|
||||
}
|
||||
|
||||
} else {
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
dtfm = dtf / mass[type[i]];
|
||||
x[i][0] += -dt * v[i][0];
|
||||
x[i][1] += -dt * v[i][1];
|
||||
x[i][2] += -dt * v[i][2];
|
||||
v[i][0] = gjffac * (wildcard[i][0] + dtfm * franprev[i][0] + dtfm * f[i][0]);
|
||||
v[i][1] = gjffac * (wildcard[i][1] + dtfm * franprev[i][1] + dtfm * f[i][1]);
|
||||
v[i][2] = gjffac * (wildcard[i][2] + dtfm * franprev[i][2] + dtfm * f[i][2]);
|
||||
x[i][0] += gjffac * dt * v[i][0];
|
||||
x[i][1] += gjffac * dt * v[i][1];
|
||||
x[i][2] += gjffac * dt * v[i][2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
|
@ -477,9 +592,8 @@ void FixLangevin::post_force_templated()
|
|||
// sum random force over all atoms in group
|
||||
// subtract sum/count from each atom in group
|
||||
|
||||
double fdrag[3],fran[3],fsum[3],fsumall[3];
|
||||
double fdrag[3],fran[3],fsum[3],fsumall[3], rantemp[3];
|
||||
bigint count;
|
||||
double fswap;
|
||||
|
||||
double boltz = force->boltz;
|
||||
double dt = update->dt;
|
||||
|
|
@ -513,7 +627,7 @@ void FixLangevin::post_force_templated()
|
|||
if (Tp_TSTYLEATOM) tsqrt = sqrt(tforce[i]);
|
||||
if (Tp_RMASS) {
|
||||
gamma1 = -rmass[i] / t_period / ftm2v;
|
||||
gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
|
||||
gamma2 = sqrt(rmass[i]) * sqrt(2.0*boltz/t_period/dt/mvv2e) / ftm2v;
|
||||
gamma1 *= 1.0/ratio[type[i]];
|
||||
gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
|
||||
} else {
|
||||
|
|
@ -521,9 +635,9 @@ void FixLangevin::post_force_templated()
|
|||
gamma2 = gfactor2[type[i]] * tsqrt;
|
||||
}
|
||||
|
||||
fran[0] = gamma2*(random->uniform()-0.5);
|
||||
fran[1] = gamma2*(random->uniform()-0.5);
|
||||
fran[2] = gamma2*(random->uniform()-0.5);
|
||||
fran[0] = gamma2*random->gaussian();
|
||||
fran[1] = gamma2*random->gaussian();
|
||||
fran[2] = gamma2*random->gaussian();
|
||||
|
||||
if (Tp_BIAS) {
|
||||
temperature->remove_bias(i,v[i]);
|
||||
|
|
@ -541,25 +655,20 @@ void FixLangevin::post_force_templated()
|
|||
}
|
||||
|
||||
if (Tp_GJF) {
|
||||
fswap = 0.5*(fran[0]+franprev[i][0]);
|
||||
franprev[i][0] = fran[0];
|
||||
fran[0] = fswap;
|
||||
fswap = 0.5*(fran[1]+franprev[i][1]);
|
||||
franprev[i][1] = fran[1];
|
||||
fran[1] = fswap;
|
||||
fswap = 0.5*(fran[2]+franprev[i][2]);
|
||||
franprev[i][2] = fran[2];
|
||||
fran[2] = fswap;
|
||||
wildcard[i][0] = f[i][0];
|
||||
wildcard[i][1] = f[i][1];
|
||||
wildcard[i][2] = f[i][2];
|
||||
|
||||
fdrag[0] *= gjffac;
|
||||
fdrag[1] *= gjffac;
|
||||
fdrag[2] *= gjffac;
|
||||
fran[0] *= gjffac;
|
||||
fran[1] *= gjffac;
|
||||
fran[2] *= gjffac;
|
||||
f[i][0] *= gjffac;
|
||||
f[i][1] *= gjffac;
|
||||
f[i][2] *= gjffac;
|
||||
rantemp[0] = fran[0];
|
||||
rantemp[1] = fran[1];
|
||||
rantemp[2] = fran[2];
|
||||
fran[0] = franprev[i][0];
|
||||
fran[1] = franprev[i][1];
|
||||
fran[2] = franprev[i][2];
|
||||
|
||||
fdrag[0] *= -2*t_period*(2*gjffac-1/gjffac-1)/dt;
|
||||
fdrag[1] *= -2*t_period*(2*gjffac-1/gjffac-1)/dt;
|
||||
fdrag[2] *= -2*t_period*(2*gjffac-1/gjffac-1)/dt;
|
||||
}
|
||||
|
||||
f[i][0] += fdrag[0] + fran[0];
|
||||
|
|
@ -567,6 +676,11 @@ void FixLangevin::post_force_templated()
|
|||
f[i][2] += fdrag[2] + fran[2];
|
||||
|
||||
if (Tp_TALLY) {
|
||||
if (Tp_GJF){
|
||||
fdrag[0] = gamma1*gjffac*v[i][0];
|
||||
fdrag[1] = gamma1*gjffac*v[i][1];
|
||||
fdrag[2] = gamma1*gjffac*v[i][2];
|
||||
}
|
||||
flangevin[i][0] = fdrag[0] + fran[0];
|
||||
flangevin[i][1] = fdrag[1] + fran[1];
|
||||
flangevin[i][2] = fdrag[2] + fran[2];
|
||||
|
|
@ -577,6 +691,19 @@ void FixLangevin::post_force_templated()
|
|||
fsum[1] += fran[1];
|
||||
fsum[2] += fran[2];
|
||||
}
|
||||
|
||||
if (Tp_GJF)
|
||||
{
|
||||
franprev[i][0] = rantemp[0];
|
||||
franprev[i][1] = rantemp[1];
|
||||
franprev[i][2] = rantemp[2];
|
||||
|
||||
if (hsflag){
|
||||
lv[i][0] = v[i][0];
|
||||
lv[i][1] = v[i][1];
|
||||
lv[i][2] = v[i][2];
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -641,9 +768,9 @@ void FixLangevin::compute_target()
|
|||
input->variable->compute_atom(tvar,igroup,tforce,1,0);
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit)
|
||||
if (tforce[i] < 0.0)
|
||||
error->one(FLERR,
|
||||
"Fix langevin variable returned negative temperature");
|
||||
if (tforce[i] < 0.0)
|
||||
error->one(FLERR,
|
||||
"Fix langevin variable returned negative temperature");
|
||||
}
|
||||
modify->addstep_compute(update->ntimestep + 1);
|
||||
}
|
||||
|
|
@ -756,20 +883,41 @@ void FixLangevin::angmom_thermostat()
|
|||
|
||||
void FixLangevin::end_of_step()
|
||||
{
|
||||
if (!tallyflag) return;
|
||||
if (!tallyflag && !gjfflag) return;
|
||||
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
energy_onestep = 0.0;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit)
|
||||
energy_onestep += flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] +
|
||||
flangevin[i][2]*v[i][2];
|
||||
|
||||
energy += energy_onestep*update->dt;
|
||||
if (mask[i] & groupbit) {
|
||||
if (gjfflag){
|
||||
f[i][0] = wildcard[i][0];
|
||||
f[i][1] = wildcard[i][1];
|
||||
f[i][2] = wildcard[i][2];
|
||||
wildcard[i][0] = v[i][0];
|
||||
wildcard[i][1] = v[i][1];
|
||||
wildcard[i][2] = v[i][2];
|
||||
if (hsflag){
|
||||
v[i][0] = lv[i][0];
|
||||
v[i][1] = lv[i][1];
|
||||
v[i][2] = lv[i][2];
|
||||
}
|
||||
}
|
||||
if (tallyflag && hsflag){
|
||||
energy_onestep += gjffac*(flangevin[i][0] * lv[i][0] +
|
||||
flangevin[i][1] * lv[i][1] + flangevin[i][2] * lv[i][2]);
|
||||
}
|
||||
else if (tallyflag){
|
||||
energy_onestep += flangevin[i][0] * v[i][0] + flangevin[i][1] * v[i][1] +
|
||||
flangevin[i][2] * v[i][2];
|
||||
}
|
||||
}
|
||||
if (tallyflag) {
|
||||
energy += energy_onestep * update->dt;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
|
@ -869,7 +1017,8 @@ void *FixLangevin::extract(const char *str, int &dim)
|
|||
double FixLangevin::memory_usage()
|
||||
{
|
||||
double bytes = 0.0;
|
||||
if (gjfflag) bytes += atom->nmax*3 * sizeof(double);
|
||||
if (gjfflag) bytes += atom->nmax*3*2 * sizeof(double);
|
||||
if (gjfflag) if (hsflag) bytes += atom->nmax*3 * sizeof(double);
|
||||
if (tallyflag) bytes += atom->nmax*3 * sizeof(double);
|
||||
if (tforce) bytes += atom->nmax * sizeof(double);
|
||||
return bytes;
|
||||
|
|
@ -882,6 +1031,8 @@ double FixLangevin::memory_usage()
|
|||
void FixLangevin::grow_arrays(int nmax)
|
||||
{
|
||||
memory->grow(franprev,nmax,3,"fix_langevin:franprev");
|
||||
memory->grow(wildcard,nmax,3,"fix_langevin:wildcard");
|
||||
if (hsflag) memory->grow(lv,nmax,3,"fix_langevin:lv");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
|
@ -890,8 +1041,17 @@ void FixLangevin::grow_arrays(int nmax)
|
|||
|
||||
void FixLangevin::copy_arrays(int i, int j, int /*delflag*/)
|
||||
{
|
||||
for (int m = 0; m < nvalues; m++)
|
||||
franprev[j][m] = franprev[i][m];
|
||||
franprev[j][0] = franprev[i][0];
|
||||
franprev[j][1] = franprev[i][1];
|
||||
franprev[j][2] = franprev[i][2];
|
||||
wildcard[j][0] = wildcard[i][0];
|
||||
wildcard[j][1] = wildcard[i][1];
|
||||
wildcard[j][2] = wildcard[i][2];
|
||||
if (hsflag) {
|
||||
lv[j][0] = lv[i][0];
|
||||
lv[j][1] = lv[i][1];
|
||||
lv[j][2] = lv[i][2];
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
|
@ -900,8 +1060,19 @@ void FixLangevin::copy_arrays(int i, int j, int /*delflag*/)
|
|||
|
||||
int FixLangevin::pack_exchange(int i, double *buf)
|
||||
{
|
||||
for (int m = 0; m < nvalues; m++) buf[m] = franprev[i][m];
|
||||
return nvalues;
|
||||
int n = 0;
|
||||
buf[n++] = franprev[i][0];
|
||||
buf[n++] = franprev[i][1];
|
||||
buf[n++] = franprev[i][2];
|
||||
buf[n++] = wildcard[i][0];
|
||||
buf[n++] = wildcard[i][1];
|
||||
buf[n++] = wildcard[i][2];
|
||||
if (hsflag){
|
||||
buf[n++] = lv[i][0];
|
||||
buf[n++] = lv[i][1];
|
||||
buf[n++] = lv[i][2];
|
||||
}
|
||||
return n;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
|
@ -910,6 +1081,17 @@ int FixLangevin::pack_exchange(int i, double *buf)
|
|||
|
||||
int FixLangevin::unpack_exchange(int nlocal, double *buf)
|
||||
{
|
||||
for (int m = 0; m < nvalues; m++) franprev[nlocal][m] = buf[m];
|
||||
return nvalues;
|
||||
int n = 0;
|
||||
franprev[nlocal][0] = buf[n++];
|
||||
franprev[nlocal][1] = buf[n++];
|
||||
franprev[nlocal][2] = buf[n++];
|
||||
wildcard[nlocal][0] = buf[n++];
|
||||
wildcard[nlocal][1] = buf[n++];
|
||||
wildcard[nlocal][2] = buf[n++];
|
||||
if (hsflag){
|
||||
lv[nlocal][0] = buf[n++];
|
||||
lv[nlocal][1] = buf[n++];
|
||||
lv[nlocal][2] = buf[n++];
|
||||
}
|
||||
return n;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -31,6 +31,8 @@ class FixLangevin : public Fix {
|
|||
int setmask();
|
||||
void init();
|
||||
void setup(int);
|
||||
//virtual void initial_integrate(int);
|
||||
virtual void post_integrate();
|
||||
virtual void post_force(int);
|
||||
void post_force_respa(int, int, int);
|
||||
virtual void end_of_step();
|
||||
|
|
@ -46,7 +48,7 @@ class FixLangevin : public Fix {
|
|||
int unpack_exchange(int, double *);
|
||||
|
||||
protected:
|
||||
int gjfflag,oflag,tallyflag,zeroflag,tbiasflag;
|
||||
int gjfflag,oflag,tallyflag,zeroflag,tbiasflag,hsflag;
|
||||
int flangevin_allocated;
|
||||
double ascale;
|
||||
double t_start,t_stop,t_period,t_target;
|
||||
|
|
@ -63,6 +65,9 @@ class FixLangevin : public Fix {
|
|||
double **flangevin;
|
||||
double *tforce;
|
||||
double **franprev;
|
||||
double **lv; //lucas velocity or half-step velocity
|
||||
double **wildcard;
|
||||
|
||||
int nvalues;
|
||||
|
||||
char *id_temp;
|
||||
|
|
|
|||
Loading…
Reference in New Issue