Changeset 744
- Timestamp:
- 06/20/12 13:56:33 (11 months ago)
- Location:
- trunk
- Files:
-
- 2 edited
-
configure.ac (modified) (2 diffs)
-
doc/ape.texi (modified) (25 diffs)
Legend:
- Unmodified
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trunk/configure.ac
r615 r744 1 1 # Process this file with autoconf to produce a configure script. 2 2 3 ## Copyright (C) 2004-20 07M. Oliveira, F. Nogueira3 ## Copyright (C) 2004-2012 M. Oliveira, F. Nogueira 4 4 ## 5 5 ## This program is free software; you can redistribute it and/or modify … … 21 21 22 22 AC_PREREQ(2.59) 23 AC_INIT([APE],[ 1.x],[ape-devel@tddft.org],[ape])23 AC_INIT([APE],[2.x],[ape-users@tddft.org],[ape]) 24 24 AC_CONFIG_SRCDIR([src/global.F90]) 25 25 AC_CONFIG_AUX_DIR([build-aux]) -
trunk/doc/ape.texi
r743 r744 13 13 14 14 @copying 15 This manual is for APE (Atomic Pseudopotentials Engine) 1.x, a15 This manual is for APE (Atomic Pseudopotentials Engine) 2.x, a 16 16 density functional theory atomic program and pseudopotentials 17 17 generator. … … 38 38 @subtitle Atomic calculations 39 39 @subtitle Pseudopotentials generation 40 @subtitle March 201140 @subtitle June 2012 41 41 @sp 4 42 42 … … 309 309 can obtain it 310 310 @uref{http://www.tddft.org/programs/octopus/wiki/index.php/Libxc, 311 here}. You will need version 1.1 or higher.311 here}. 312 312 313 313 @end enumerate … … 353 353 export FCFLAGS="-O3 -Wall" 354 354 @end example 355 if you are using the GNU Fortran compiler on a linux machine.Also, if355 if you are using the GNU Fortran compiler on a Linux machine. Also, if 356 356 you have some of the required libraries in some unusual directories, 357 357 these directories may be placed in the variable @code{LDFLAGS} (e.g., 358 @code{export LDFLAGS= $LDFLAGS:/opt/lib/}).358 @code{export LDFLAGS="-L/opt/lib/"}). 359 359 360 360 … … 386 386 library is installed, the program @code{gsl-config} should be 387 387 somewhere.) 388 @item 388 389 @code{--with-libxc-prefix=DIR}: Installation directory of the @sc{libxc} 389 390 library. The libraries are expected to be in @code{DIR/lib} and the … … 391 392 @end itemize 392 393 393 Run @code{make}, and then @code{make install}. If everything went fine, 394 you should now be able to run @code{APE}. 394 Run @code{make}, and then @code{make check}. This last command will 395 launch the @code{APE} testsuite. If all tests were passed, you can 396 then install the code with @code{make install}. If everything went 397 fine, you should now be able to run @code{APE}. 395 398 396 399 The program has been tested in the following platforms: … … 409 412 of this document is in the @code{APE-HOME/doc} directory. 410 413 414 415 411 416 @node Troubleshooting, , Long instructions, Installation 412 417 @section Troubleshooting … … 415 420 wrong. 416 421 422 @strong{Some tests of the testsuite fail}: When running the testsuite, one 423 or more tests fail. 424 425 @itemize @bullet 426 427 @item Is the test failing because of a very small numerical difference? 428 While running a test, if a test case is failed, the code will print 429 some extra information about the failure, namely the calculated value, 430 the reference value, and the allowed tolerance. This should look like 431 this: 432 @example 433 434 Match Failed 435 Calculated value : -24.344302 436 Reference value : -24.344198 437 Difference : 0.000104 438 Tolerance : 8e-5 439 440 @end example 441 If the difference is slightly larger than the tolerance, like in the 442 previous example, and if the same happens for all the failed test 443 cases, then it is likely that there is nothing wrong with your 444 compilation. 445 446 @end itemize 447 448 417 449 @strong{Could not find GSL library}: We assume that you have already 418 installed @code{GSL} but, for some reason, you were not able to compile419 the code.450 installed @code{GSL} but, for some reason, you were not able to 451 compile the code. 420 452 421 453 @itemize @bullet … … 642 674 @item @code{pp}: Pseudopotential generation. 643 675 @item @code{pp_test}: Pseudopotential test. 676 @item @code{xc}: One-shot evaluation of exchange and correlation energies and potentials. 677 @item @code{ip}: Calculation of ionization energy. 678 @item @code{nt}: Numerical tests. Should only be useful to developers. 644 679 @end itemize 645 680 … … 729 764 @vindex @code{XCFunctional} 730 765 731 The possible values are: 766 The possible values are (note that, depending on the version of 767 @code{libxc} used, some of the following functionals might not be 768 available): 732 769 @itemize @bullet 733 770 @item @code{none}: No exchange-correlation. … … 865 902 866 903 The first and second columns are the main quantum number @emph{n} and 867 the angular momentum quantum number @emph{l}. The remaining columns are 868 used to specify the occupancies. One or two columns can be used to 869 specify the occupancies and there are four possible cases: 904 the angular momentum quantum number @emph{l}. The meaning of the 905 remaining columns depends if we are running a fully-relativistic 906 spin-polarized calculation or not. In the later case, the remaining 907 columns are used to specify the occupancies. One or two columns can be 908 used to specify the occupancies and there are four possible cases: 870 909 871 910 @itemize @bullet … … 886 925 887 926 @end itemize 927 928 When running a fully-relativistic spin-polarized calculation 929 (@code{WaveEquation = dirac} and @code{SpinMode = polarized}), besides 930 the @emph{n} and @emph{l} quantum numbers, it is also necessary to 931 specify the @emph{m} quantum number, which will always be the third 932 column of the block. This quantum number runs from @emph{-j} to 933 @emph{j}, where @emph{j} can have two values: @emph{j = l - 1/2} and 934 @emph{j = l + 1/2}. This means that, when @emph{|m| < l+1/2} there 935 will be two orbitals with the same @emph{m} quantum number. To 936 differentiate these two orbitals, a fourth quantum number is 937 introduced, which can have two values: @emph{up} or @emph{down} (these 938 are represented in @code{APE} by @emph{0.5} and @emph{-0.5}). The 939 meaning of the columns beyond the third is thus the following: 940 941 @itemize @bullet 942 @item If @emph{|m| = 2l+1}: the fourth column is just the occupancy. 943 944 @item If @emph{|m| < 2l+1}: the fourth column is the occupancy of 945 the @emph{up} orbital and the fifth column is the occupancy of the 946 @emph{down} orbital. If only the fourth column is set, both orbitals 947 are equally occupied with half the specified value. 948 949 @end itemize 950 951 888 952 889 953 Note that the occupancies can be set to zero. … … 900 964 The first column sets the quantum number @emph{n}, the second the 901 965 quantum number @emph{l} and the last two the occupancies for both spin 902 channels. 903 966 channels. In case of a fully-relativistic spin-polarized calculation, 967 the previous example would become: 968 @example 969 %Orbitals 970 1 | 0 | -1/2 | 1 971 1 | 0 | 1/2 | 1 972 1 | 1 | -1/2 | 1 973 1 | 1 | 1/2 | 0 974 2 | 1 | -3/2 | 0 975 2 | 1 | -1/2 | 0 | 0 976 2 | 1 | 1/2 | 0 | 0 977 2 | 1 | 3/2 | 0 978 % 979 @end example 904 980 905 981 To make things easier, the core configuration can be replaced by a … … 913 989 % 914 990 @end example 915 916 991 917 992 … … 1362 1437 APE - Atomic Pseudopotentials Engine 1363 1438 1364 Program started on 201 0/10/28 at 15:03:371439 Program started on 2012/06/20 at 12:01:41 1365 1440 1366 1441 Compilation Info 1367 Version: 1.x1442 Version: 2.x 1368 1443 Revision: 1369 Build time: Tue Oct 26 14:25:55 WEST 20101444 Build time: Wed Jun 20 12:00:49 WEST 2012 1370 1445 C compiler: gcc 1371 1446 C compiler flags: -g -O2 -I/usr/include 1372 1447 Fortran compiler: gfortran 1373 Fortran compiler flags: - g -O21448 Fortran compiler flags: -Wall -fbounds-check 1374 1449 1375 1450 Calculation Type: … … 1380 1455 Output units system: Atomic Units 1381 1456 1382 Initializing Wave-Equations Integrator1383 Stepping function: Embedded 8th order Runge-Kutta Prince-Dormand1384 method with 9th order error estimate1385 ODE Integrator tolerance: 1.000E-061386 ODE Integrator maximum number of steps: 500001387 ODE Integrator minimum step size: 1.000E-151388 1389 1457 Eigensolver Info 1390 1458 Method: Brent's method 1391 Tolerance: 1.000E-0 51459 Tolerance: 1.000E-08 1392 1460 1393 1461 1394 1462 -- All Electron Calculation -- 1395 1463 1464 Initializing ODE Integrator 1465 ODE Stepping function: Embedded 8th order Runge-Kutta Prince-Dormand 1466 method with 9th order error estimate 1467 ODE Integrator tolerance: 1.000E-12 1468 ODE Integrator maximum number of steps: 500000 1469 1396 1470 General Information about the atom: 1397 Non relativistic spin-unpolarized calculations for Li 1398 Nuclear charge : 3.00 1399 Total charge : 0.00 1471 Symbol: Li 1472 Theory Level: DFT 1473 Wave-equation: Schrodinger 1474 Spin mode: unpolarized 1475 Nuclear charge: 3.00 1476 Total charge: 0.00 1400 1477 Configuration : State Occupation 1401 1478 1s 2.00 … … 1412 1489 Mesh outmost point: 51.962 b 1413 1490 Mesh parameters (a, b): 7.49453E-02, 1.60699E-05 1491 Mesh number of points: 200 1492 Derivatives Method: Cubic slines 1414 1493 1415 1494 Starting SCF process 1416 1495 Convergence tolerance: ConvAbsDens ConvRelDens 1417 1.000E-05 0.000E+001418 ConvAbsE vsum ConvRelEvsum1496 0.000E+00 1.000E-08 1497 ConvAbsEnergy ConvRelEnergy 1419 1498 0.000E+00 0.000E+00 1420 Maximum number of iterations: 100 1499 Smearing: fixed occupancies 1500 Maximum number of iterations: 300 1421 1501 Mixing scheme: Modified Broyden's Method 1422 1423 Performing SCF Run 1502 Mixing: 0.300 1503 1504 Performing SCF Cycle 1424 1505 1425 1506 Final results for SCF procedure: 1426 Eigenvalues [H] 1427 State Occupation Eigenvalue 1428 1s 2.00 -1.87822 1429 2s 1.00 -0.10559 1430 2p 0.00 -0.04139 1431 1432 Program finished on 2010/10/28 at 15:03:38 1507 1508 Program finished on 2012/06/20 at 12:01:42 1433 1509 1434 1510 @end example … … 1439 1515 @example 1440 1516 1441 drwxrwxr-x 2 user group 4096 201 0-10-28 15:03ae1442 -rw-rw-r-- 1 user group 198 201 0-10-28 15:03inp.ape1443 -rw-rw-r-- 1 user group 1 135 2010-10-28 15:03parser.log1517 drwxrwxr-x 2 user group 4096 2012-06-20 12:01 ae 1518 -rw-rw-r-- 1 user group 198 2012-06-20 12:01 inp.ape 1519 -rw-rw-r-- 1 user group 1022 2012-06-20 12:01 parser.log 1444 1520 1445 1521 @end example … … 1449 1525 @example 1450 1526 1451 -rw-r--r-- 1 user group 24714 2010-10-28 15:03 data 1452 -rw-r--r-- 1 user group 14665 2010-10-28 15:03 density 1453 -rw-r--r-- 1 user group 1453 2010-10-28 15:03 info 1454 -rw-r--r-- 1 user group 7396 2010-10-28 15:03 tau 1455 -rw-r--r-- 1 user group 7567 2010-10-28 15:03 v_c 1456 -rw-r--r-- 1 user group 7361 2010-10-28 15:03 v_ext 1457 -rw-r--r-- 1 user group 7361 2010-10-28 15:03 v_hxc 1458 -rw-r--r-- 1 user group 7567 2010-10-28 15:03 v_x 1459 -rw-r--r-- 1 user group 7361 2010-10-28 15:03 v_xctau 1460 -rw-r--r-- 1 user group 10937 2010-10-28 15:03 wf-1s 1461 -rw-r--r-- 1 user group 10937 2010-10-28 15:03 wf-2p 1462 -rw-r--r-- 1 user group 10965 2010-10-28 15:03 wf-2s 1527 -rw-r--r-- 1 user group 24885 2012-06-20 12:01 data 1528 -rw-r--r-- 1 user group 14665 2012-06-20 12:01 density 1529 -rw-r--r-- 1 user group 1549 2012-06-20 12:01 info 1530 -rw-r--r-- 1 user group 7396 2012-06-20 12:01 tau 1531 -rw-r--r-- 1 user group 7567 2012-06-20 12:01 v_c 1532 -rw-r--r-- 1 user group 7361 2012-06-20 12:01 v_ext 1533 -rw-r--r-- 1 user group 7361 2012-06-20 12:01 v_hxc 1534 -rw-r--r-- 1 user group 7567 2012-06-20 12:01 v_x 1535 -rw-r--r-- 1 user group 10938 2012-06-20 12:01 wf-1s 1536 -rw-r--r-- 1 user group 10938 2012-06-20 12:01 wf-2p 1537 -rw-r--r-- 1 user group 10966 2012-06-20 12:01 wf-2s 1463 1538 1464 1539 @end example … … 1494 1569 @example 1495 1570 1496 APE - Atomic Pseudopotentials Engine1497 1498 Program started on 201 0/10/28 at 15:09:361571 APE - Atomic Pseudopotentials Engine 1572 1573 Program started on 2012/06/20 at 12:06:13 1499 1574 1500 1575 Compilation Info 1501 Version: 1.x1576 Version: 2.x 1502 1577 Revision: 1503 Build time: Tue Oct 26 14:25:55 WEST 20101578 Build time: Wed Jun 20 12:00:49 WEST 2012 1504 1579 C compiler: gcc 1505 1580 C compiler flags: -g -O2 -I/usr/include 1506 1581 Fortran compiler: gfortran 1507 Fortran compiler flags: - g -O21582 Fortran compiler flags: -Wall -fbounds-check 1508 1583 1509 1584 Calculation Type: … … 1514 1589 Output units system: Atomic Units 1515 1590 1516 Initializing Wave-Equations Integrator1517 Stepping function: Embedded 8th order Runge-Kutta Prince-Dormand1518 method with 9th order error estimate1519 ODE Integrator tolerance: 1.000E-061520 ODE Integrator maximum number of steps: 500001521 ODE Integrator minimum step size: 1.000E-151522 1523 1591 Eigensolver Info 1524 1592 Method: Brent's method 1525 Tolerance: 1.000E-05 1593 Tolerance: 1.000E-08 1594 1595 Initializing ODE Integrator 1596 ODE Stepping function: Embedded 8th order Runge-Kutta Prince-Dormand 1597 method with 9th order error estimate 1598 ODE Integrator tolerance: 1.000E-12 1599 ODE Integrator maximum number of steps: 500000 1526 1600 1527 1601 … … 1536 1610 Pseudopotential Generation: 1537 1611 State: 2s 1538 Scheme 1612 Scheme: Hamann 1539 1613 Core radius: 1.807 Matching Radius: 5.486 1540 cl = 0.1270 5447691614 cl = 0.1270413205 1541 1615 State: 2p 1542 Scheme 1616 Scheme: Hamann 1543 1617 Core radius: 1.509 Matching Radius: 4.381 1544 cl = -0.9176 0349761618 cl = -0.9176124519 1545 1619 1546 1620 Pseudopotentials Self-Consistency: 1547 1621 State Eigenvalue [H ] Norm Test Slope Test 1548 2s -0.105 59 1.0000049 1.00000341549 2p -0.041 39 0.9998834 0.99981741622 2s -0.10560 1.0000049 0.9999925 1623 2p -0.04140 0.9998835 0.9998173 1550 1624 1551 1625 Kleinman & Bylander Atom 1552 1626 Local potential is a Vanderbilt function 1553 1627 z rcmax v0 v1 v2 v3 1554 1.00 1.81 -1.383908 -0.459303 0.070320 -0.0047851628 1.00 5.09 -0.491383 -0.057906 0.001118 -0.000010 1555 1629 Non-local components: 1556 1630 State KB Energy [H ] KB Cosine 1557 2s 0.6711 0.25151558 2p -0. 3222 -0.18321631 2s 1.0840 0.0761 1632 2p -0.4609 -0.2732 1559 1633 1560 1634 Ghost state analysis: 1561 1635 State: 2s 1562 1636 KB energy > 0; E0 < Eref < E1 => No ghost states 1563 Local potential eigenvalues: -0. 2464 (E0) -0.0213(E1)1637 Local potential eigenvalues: -0.1215 (E0) -0.0050 (E1) 1564 1638 Reference energy: -0.1056 (Eref) 1565 1639 State: 2p 1566 1640 KB energy < 0; Eref < E0 => No ghost states 1567 Local potential eigenvalues: -0.0 340(E0) 0.0000 (E1)1641 Local potential eigenvalues: -0.0248 (E0) 0.0000 (E1) 1568 1642 Reference energy: -0.0414 (Eref) 1569 1643 1570 1644 Localization radii [b]: 1571 Local: 1.421572 l = 0: 3.251573 l = 1: 2.791574 1575 Program finished on 201 0/10/28 at 15:09:371645 Local: 3.77 1646 l = 0: 4.06 1647 l = 1: 3.77 1648 1649 Program finished on 2012/06/20 at 12:06:14 1576 1650 1577 1651 @end example … … 1584 1658 @example 1585 1659 1586 -rw-r--r-- 1 user group 26281 2010-10-28 15:09 data 1587 -rw-r--r-- 1 user group 14665 2010-10-28 15:09 density 1588 -rw-r--r-- 1 user group 690 2010-10-28 15:09 info 1589 -rw-r--r-- 1 user group 7361 2010-10-28 15:09 pp-p 1590 -rw-r--r-- 1 user group 7361 2010-10-28 15:09 pp-s 1591 -rw-r--r-- 1 user group 7396 2010-10-28 15:09 tau 1592 -rw-r--r-- 1 user group 7567 2010-10-28 15:09 v_c 1593 -rw-r--r-- 1 user group 7361 2010-10-28 15:09 v_hxc 1594 -rw-r--r-- 1 user group 7567 2010-10-28 15:09 v_x 1595 -rw-r--r-- 1 user group 7361 2010-10-28 15:09 v_xctau 1596 -rw-r--r-- 1 user group 10937 2010-10-28 15:09 wf-2p 1597 -rw-r--r-- 1 user group 10937 2010-10-28 15:09 wf-2s 1660 -rw-r--r-- 1 user group 26463 2012-06-20 12:06 data 1661 -rw-r--r-- 1 user group 14665 2012-06-20 12:06 density 1662 -rw-r--r-- 1 user group 696 2012-06-20 12:06 info 1663 -rw-r--r-- 1 user group 7361 2012-06-20 12:06 pp-p 1664 -rw-r--r-- 1 user group 7361 2012-06-20 12:06 pp-s 1665 -rw-r--r-- 1 user group 7396 2012-06-20 12:06 tau 1666 -rw-r--r-- 1 user group 7567 2012-06-20 12:06 v_c 1667 -rw-r--r-- 1 user group 7361 2012-06-20 12:06 v_hxc 1668 -rw-r--r-- 1 user group 7567 2012-06-20 12:06 v_x 1669 -rw-r--r-- 1 user group 10938 2012-06-20 12:06 wf-2p 1670 -rw-r--r-- 1 user group 10938 2012-06-20 12:06 wf-2s 1598 1671 1599 1672 @end example … … 1614 1687 @example 1615 1688 1616 -rw-r--r-- 1 user group 819 2010-10-28 15:09 info 1617 -rw-r--r-- 1 user group 7361 2010-10-28 15:09 kb-local 1618 -rw-r--r-- 1 user group 7364 2010-10-28 15:09 kb-p 1619 -rw-r--r-- 1 user group 7364 2010-10-28 15:09 kb-s 1620 -rw-r--r-- 1 user group 7567 2010-10-28 15:09 v_c 1621 -rw-r--r-- 1 user group 7567 2010-10-28 15:09 v_x 1689 -rw-r--r-- 1 user group 819 2012-06-20 12:06 info 1690 -rw-r--r-- 1 user group 7361 2012-06-20 12:06 kb-local 1691 -rw-r--r-- 1 user group 7364 2012-06-20 12:06 kb-p 1692 -rw-r--r-- 1 user group 7364 2012-06-20 12:06 kb-s 1622 1693 1623 1694 @end example … … 1626 1697 projectors and it should be self-explanatory. The file @code{kb-local} 1627 1698 contains the local component used to generated the Kleinman-Bylander 1628 projectors, while the other @code{kb} files contain the projectors. The 1629 remaning files do not contain for the moment any relevant information. 1699 projectors, while the other @code{kb} files contain the projectors. 1700 1701 1702 After generating the pseudopotentials, one should test them. One 1703 simple test is to compare the logarithmic derivative of the 1704 wavefunctions as a function of the orbital energy at a given 1705 diagnostic radius. The following input file will to precisely that: 1706 @example 1707 1708 Title = "Lithium" 1709 CalculationMode = pp_test 1710 Verbose = 30 1711 1712 PPTests = ld 1713 1714 @end example 1715 1716 In this case the output should look like this: 1717 @example 1718 1719 APE - Atomic Pseudopotentials Engine 1720 1721 Program started on 2012/06/20 at 13:55:25 1722 1723 Compilation Info 1724 Version: 2.x 1725 Revision: 1726 Build time: Wed Jun 20 12:00:49 WEST 2012 1727 C compiler: gcc 1728 C compiler flags: -g -O2 -I/usr/include 1729 Fortran compiler: gfortran 1730 Fortran compiler flags: -Wall -fbounds-check 1731 1732 Calculation Type: 1733 PseudoPotential Test 1734 1735 Setting units 1736 Input units system: Atomic Units 1737 Output units system: Atomic Units 1738 1739 Eigensolver Info 1740 Method: Brent's method 1741 Tolerance: 1.000E-08 1742 1743 Initializing ODE Integrator 1744 ODE Stepping function: Embedded 8th order Runge-Kutta Prince-Dormand 1745 method with 9th order error estimate 1746 ODE Integrator tolerance: 1.000E-12 1747 ODE Integrator maximum number of steps: 500000 1748 1749 1750 -- Pseudopotential Testing -- 1751 1752 Initializing ODE Integrator 1753 ODE Stepping function: Embedded 8th order Runge-Kutta Prince-Dormand 1754 method with 9th order error estimate 1755 ODE Integrator tolerance: 1.000E-12 1756 ODE Integrator maximum number of steps: 500000 1757 1758 Logarithmic Derivatives: 1759 Diagnostic radius: 2.320 b 1760 Energy step: Adaptive 1761 Computing logarithmic derivative for states: s 1762 Minimum energy: -1.106 H 1763 Maximum energy: 0.894 H 1764 Computing logarithmic derivative for states: p 1765 Minimum energy: -1.041 H 1766 Maximum energy: 0.959 H 1767 1768 Program finished on 2012/06/20 at 13:55:25 1769 1770 @end example 1771 1772 Notice that the choice of energy range and diagnostic radius was done 1773 automatically (check the description of the corresponding variable for 1774 more information about how this is done). At the end of the run there 1775 should be a new directory named @code{tests}. This directory should 1776 contain the following files: 1777 @example 1778 1779 -rw-r--r-- 1 user group 297 2012-06-20 13:55 info 1780 -rw-r--r-- 1 user group 3916 2012-06-20 13:55 ld-p 1781 -rw-r--r-- 1 user group 3700 2012-06-20 13:55 ld-s 1782 1783 @end example 1784 1785 The file @code{info} contains some information about the tests and it 1786 should be self-explanatory. The files @code{ld-} contain the 1787 all-electron and pseudo wavefunction logarithmic derivatives 1788 as a function of the orbital energy. 1789 1630 1790 1631 1791
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