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/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
gromacs-2021~beta2/src/testutils/copy_xsl.sh-4-# invoked.
gromacs-2021~beta2/src/testutils/copy_xsl.sh:5:cd `dirname $0`
gromacs-2021~beta2/src/testutils/copy_xsl.sh-6-cd ../../
##############################################
gromacs-2021~beta2/src/external/tng_io/src/lib/tng_io-config.cmake.in-2-
gromacs-2021~beta2/src/external/tng_io/src/lib/tng_io-config.cmake.in:3:include(${CMAKE_CURRENT_LIST_DIR}/tng_io.cmake)
gromacs-2021~beta2/src/external/tng_io/src/lib/tng_io-config.cmake.in-4-
##############################################
gromacs-2021~beta2/src/external/tng_io/external/zlib/crc32.c-187-/* =========================================================================
gromacs-2021~beta2/src/external/tng_io/external/zlib/crc32.c:188: * This function can be used by asm versions of crc32()
gromacs-2021~beta2/src/external/tng_io/external/zlib/crc32.c-189- */
##############################################
gromacs-2021~beta2/src/external/tng_io/external/zlib/zlib.h-1118- 8: DEBUG
gromacs-2021~beta2/src/external/tng_io/external/zlib/zlib.h:1119: 9: ASMV or ASMINF -- use ASM code
gromacs-2021~beta2/src/external/tng_io/external/zlib/zlib.h-1120- 10: ZLIB_WINAPI -- exported functions use the WINAPI calling convention
##############################################
gromacs-2021~beta2/src/external/tng_io/external/zlib/deflate.c-88-#ifdef ASMV
gromacs-2021~beta2/src/external/tng_io/external/zlib/deflate.c:89: void match_init OF((void)); /* asm code initialization */
gromacs-2021~beta2/src/external/tng_io/external/zlib/deflate.c-90- uInt longest_match OF((deflate_state *s, IPos cur_match));
##############################################
gromacs-2021~beta2/src/external/tng_io/external/zlib/deflate.c-1128-#ifdef ASMV
gromacs-2021~beta2/src/external/tng_io/external/zlib/deflate.c:1129: match_init(); /* initialize the asm code */
gromacs-2021~beta2/src/external/tng_io/external/zlib/deflate.c-1130-#endif
##############################################
gromacs-2021~beta2/src/external/tng_io/external/zlib/deflate.c-1144-#ifndef ASMV
gromacs-2021~beta2/src/external/tng_io/external/zlib/deflate.c:1145:/* For 80x86 and 680x0, an optimized version will be provided in match.asm or
gromacs-2021~beta2/src/external/tng_io/external/zlib/deflate.c-1146- * match.S. The code will be functionally equivalent.
##############################################
gromacs-2021~beta2/src/external/clFFT/src/library/lifetime.cpp-55- // Initialize function pointers to call into the shared module
gromacs-2021~beta2/src/external/clFFT/src/library/lifetime.cpp:56: PFGETSTATTIMER pfGetStatTimer = reinterpret_cast< PFGETSTATTIMER > ( LoadFunctionAddr( fftRepo.timerHandle, "getStatTimer" ) );
gromacs-2021~beta2/src/external/clFFT/src/library/lifetime.cpp-57-
##############################################
gromacs-2021~beta2/src/external/clFFT/src/include/sharedLibrary.h-91-// is returned. If the module handle is NULL, NULL is returned.
gromacs-2021~beta2/src/external/clFFT/src/include/sharedLibrary.h:92:inline void* LoadFunctionAddr( void* libHandle, std::string funcName )
gromacs-2021~beta2/src/external/clFFT/src/include/sharedLibrary.h-93-{
##############################################
gromacs-2021~beta2/src/external/clFFT/src/clFFTConfig.cmake.in:1:include(${CMAKE_CURRENT_LIST_DIR}/clFFTTargets.cmake)
gromacs-2021~beta2/src/external/clFFT/src/clFFTConfig.cmake.in-2-get_filename_component(CLFFT_INCLUDE_DIRS ${CMAKE_CURRENT_LIST_DIR}/@reldir@/include ABSOLUTE)
##############################################
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/gcc_x86.h-123- /* volatile because we read and write back to the same variable in the
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/gcc_x86.h:124: asm section. some compilers requires this to be volatile */
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/gcc_x86.h-125- __asm__ __volatile__("lock ; xaddl %0, %1;" /* swap-add */
##############################################
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/fujitsu_sparc64.h-37-
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/fujitsu_sparc64.h:38:#define tMPI_Atomic_memory_barrier() { asm ("membar #StoreStore | #LoadStore | #LoadLoad | #StoreLoad "); }
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/fujitsu_sparc64.h:39:#define tMPI_Atomic_memory_barrier_acq() { asm ("membar #StoreStore | #StoreLoad "); }
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/fujitsu_sparc64.h:40:#define tMPI_Atomic_memory_barrier_rel() { asm ("membar #LoadStore | #StoreStore "); }
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/fujitsu_sparc64.h-41-#define TMPI_HAVE_ACQ_REL_BARRIERS
##############################################
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/fujitsu_sparc64.h-71-{
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/fujitsu_sparc64.h:72: asm ("cas [%2], %1, %0"
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/fujitsu_sparc64.h-73- : "=&r" (newval)
##############################################
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/fujitsu_sparc64.h-82-{
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/fujitsu_sparc64.h:83: asm ("casx [%2], %1, %0 "
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/fujitsu_sparc64.h-84- : "=&r" (newval)
##############################################
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/gcc_ia64.h-73- volatile int res;
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/gcc_ia64.h:74: asm volatile ("xchg4 %0=[%1],%2" :
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/gcc_ia64.h-75- "=r" (res) : "r" (&a->value), "r" (b) : "memory");
##############################################
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/gcc_ia64.h-84-
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/gcc_ia64.h:85: asm volatile ("xchg8 %0=[%1],%2" :
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/gcc_ia64.h-86- "=r" (res) : "r" (&a->value), "r" (b) : "memory");
##############################################
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/gcc_ia64.h-133-/* ia64 memory barrier */
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/gcc_ia64.h:134:#define tMPI_Atomic_memory_barrier() asm volatile ("mf" ::: "memory")
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/gcc_ia64.h-135-
##############################################
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/gcc_ia64.h-140- volatile int res;
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/gcc_ia64.h:141: asm volatile ("mov ar.ccv=%0;;" :: "rO" (oldval));
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/gcc_ia64.h:142: asm volatile ("cmpxchg4.acq %0=[%1],%2,ar.ccv" :
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/gcc_ia64.h-143- "=r" (res) : "r" (&a->value), "r" (newval) : "memory");
##############################################
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/gcc_ia64.h-156- void* volatile* res;
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/gcc_ia64.h:157: asm volatile ("mov ar.ccv=%0;;" :: "rO" (oldval));
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/gcc_ia64.h:158: asm volatile ("cmpxchg8.acq %0=[%1],%2,ar.ccv" :
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/gcc_ia64.h-159- "=r" (res) : "r" (&a->value), "r" (newval) : "memory");
##############################################
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/gcc_ia64.h-170- ({ unsigned long res; \
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/gcc_ia64.h:171: asm volatile ("fetchadd4.rel %0=[%1],%2" \
gromacs-2021~beta2/src/external/thread_mpi/include/thread_mpi/atomic/gcc_ia64.h-172- : "=r" (res) : "r" (a), "r" (inc) : "memory"); \
##############################################
gromacs-2021~beta2/src/external/googletest/googlemock/CMakeLists.txt-21-# Defines pre_project_set_up_hermetic_build() and set_up_hermetic_build().
gromacs-2021~beta2/src/external/googletest/googlemock/CMakeLists.txt:22:include("${gtest_dir}/cmake/hermetic_build.cmake" OPTIONAL)
gromacs-2021~beta2/src/external/googletest/googlemock/CMakeLists.txt-23-
##############################################
gromacs-2021~beta2/src/external/googletest/googlemock/README.md-146-
gromacs-2021~beta2/src/external/googletest/googlemock/README.md:147:Suppose you put Google Mock in directory `${GMOCK_DIR}` and Google Test
gromacs-2021~beta2/src/external/googletest/googlemock/README.md:148:in `${GTEST_DIR}` (the latter is `${GMOCK_DIR}/gtest` by default). To
gromacs-2021~beta2/src/external/googletest/googlemock/README.md-149-build Google Mock, create a library build target (or a project as
##############################################
gromacs-2021~beta2/src/external/googletest/googletest/src/gtest.cc-3174- } else {
gromacs-2021~beta2/src/external/googletest/googletest/src/gtest.cc:3175: printf(", where %s = %s\n", kTypeParamLabel, test_case.type_param());
gromacs-2021~beta2/src/external/googletest/googletest/src/gtest.cc-3176- }
##############################################
gromacs-2021~beta2/src/external/googletest/googletest/src/gtest.cc-5426- // the output easy to parse by a program.
gromacs-2021~beta2/src/external/googletest/googletest/src/gtest.cc:5427: PrintOnOneLine(test_case->type_param(), kMaxParamLength);
gromacs-2021~beta2/src/external/googletest/googletest/src/gtest.cc-5428- }
##############################################
gromacs-2021~beta2/src/external/googletest/googletest/src/gtest.cc-5435- // output easy to parse by a program.
gromacs-2021~beta2/src/external/googletest/googletest/src/gtest.cc:5436: PrintOnOneLine(test_info->value_param(), kMaxParamLength);
gromacs-2021~beta2/src/external/googletest/googletest/src/gtest.cc-5437- }
##############################################
gromacs-2021~beta2/src/external/googletest/googletest/docs/PumpManual.md-48-
gromacs-2021~beta2/src/external/googletest/googletest/docs/PumpManual.md:49:The following Pump code (where meta keywords start with `$`, `[[` and `]]` are meta brackets, and `$$` starts a meta comment that ends with the line):
gromacs-2021~beta2/src/external/googletest/googletest/docs/PumpManual.md-50-
##############################################
gromacs-2021~beta2/src/external/googletest/googletest/docs/PumpManual.md-121-
gromacs-2021~beta2/src/external/googletest/googletest/docs/PumpManual.md:122:| `$var id = exp` | Defines a named constant value. `$id` is valid util the end of the current meta lexical block. |
gromacs-2021~beta2/src/external/googletest/googletest/docs/PumpManual.md-123-|:----------------|:-----------------------------------------------------------------------------------------------|
gromacs-2021~beta2/src/external/googletest/googletest/docs/PumpManual.md:124:| `$range id exp..exp` | Sets the range of an iteration variable, which can be reused in multiple loops later. |
gromacs-2021~beta2/src/external/googletest/googletest/docs/PumpManual.md:125:| `$for id sep [[ code ]]` | Iteration. The range of `id` must have been defined earlier. `$id` is valid in `code`. |
gromacs-2021~beta2/src/external/googletest/googletest/docs/PumpManual.md:126:| `$($)` | Generates a single `$` character. |
gromacs-2021~beta2/src/external/googletest/googletest/docs/PumpManual.md:127:| `$id` | Value of the named constant or iteration variable. |
gromacs-2021~beta2/src/external/googletest/googletest/docs/PumpManual.md:128:| `$(exp)` | Value of the expression. |
gromacs-2021~beta2/src/external/googletest/googletest/docs/PumpManual.md:129:| `$if exp [[ code ]] else_branch` | Conditional. |
gromacs-2021~beta2/src/external/googletest/googletest/docs/PumpManual.md-130-| `[[ code ]]` | Meta lexical block. |
gromacs-2021~beta2/src/external/googletest/googletest/docs/PumpManual.md-131-| `cpp_code` | Raw C++ code. |
gromacs-2021~beta2/src/external/googletest/googletest/docs/PumpManual.md:132:| `$$ comment` | Meta comment. |
gromacs-2021~beta2/src/external/googletest/googletest/docs/PumpManual.md-133-
gromacs-2021~beta2/src/external/googletest/googletest/docs/PumpManual.md-134-**Note:** To give the user some freedom in formatting the Pump source
gromacs-2021~beta2/src/external/googletest/googletest/docs/PumpManual.md:135:code, Pump ignores a new-line character if it's right after `$for foo`
gromacs-2021~beta2/src/external/googletest/googletest/docs/PumpManual.md-136-or next to `[[` or `]]`. Without this rule you'll often be forced to write
##############################################
gromacs-2021~beta2/src/external/googletest/googletest/docs/PumpManual.md-175-
gromacs-2021~beta2/src/external/googletest/googletest/docs/PumpManual.md:176: * If a meta variable is followed by a letter or digit, you can separate them using `[[]]`, which inserts an empty string. For example `Foo$j[[]]Helper` generate `Foo1Helper` when `j` is 1.
gromacs-2021~beta2/src/external/googletest/googletest/docs/PumpManual.md-177- * To avoid extra-long Pump source lines, you can break a line anywhere you want by inserting `[[]]` followed by a new line. Since any new-line character next to `[[` or `]]` is ignored, the generated code won't contain this new line.
##############################################
gromacs-2021~beta2/src/external/googletest/googletest/README.md-10-
gromacs-2021~beta2/src/external/googletest/googletest/README.md:11:Suppose you put Google Test in directory `${GTEST_DIR}`. To build it, create a
gromacs-2021~beta2/src/external/googletest/googletest/README.md-12-library build target (or a project as called by Visual Studio and Xcode) to
##############################################
gromacs-2021~beta2/src/external/googletest/googletest/README.md-16-
gromacs-2021~beta2/src/external/googletest/googletest/README.md:17:with `${GTEST_DIR}/include` in the system header search path and `${GTEST_DIR}`
gromacs-2021~beta2/src/external/googletest/googletest/README.md-18-in the normal header search path. Assuming a Linux-like system and gcc,
##############################################
gromacs-2021~beta2/src/external/googletest/googletest/README.md-26-
gromacs-2021~beta2/src/external/googletest/googletest/README.md:27:Next, you should compile your test source file with `${GTEST_DIR}/include` in
gromacs-2021~beta2/src/external/googletest/googletest/README.md-28-the system header search path, and link it with gtest and any other necessary
##############################################
gromacs-2021~beta2/src/external/googletest/googletest/cmake/Config.cmake.in-7-
gromacs-2021~beta2/src/external/googletest/googletest/cmake/Config.cmake.in:8:include("${CMAKE_CURRENT_LIST_DIR}/@targets_export_name@.cmake")
gromacs-2021~beta2/src/external/googletest/googletest/cmake/Config.cmake.in-9-check_required_components("@project_name@")
##############################################
gromacs-2021~beta2/src/gromacs/gpu_utils/device_utils.clh-51-
gromacs-2021~beta2/src/gromacs/gpu_utils/device_utils.clh:52:/* \brief Atomically increment the float value at address addr (in local memory) with value val.
gromacs-2021~beta2/src/gromacs/gpu_utils/device_utils.clh-53- *
##############################################
gromacs-2021~beta2/src/gromacs/gpu_utils/device_utils.clh-73-
gromacs-2021~beta2/src/gromacs/gpu_utils/device_utils.clh:74:/* \brief Atomically increment the float3 value at address addr (in local memory) with value val.
gromacs-2021~beta2/src/gromacs/gpu_utils/device_utils.clh-75- *
##############################################
gromacs-2021~beta2/src/gromacs/gpu_utils/device_utils.clh-89-
gromacs-2021~beta2/src/gromacs/gpu_utils/device_utils.clh:90:/* \brief Atomically increment the float value at address addr (in global memory) with value val.
gromacs-2021~beta2/src/gromacs/gpu_utils/device_utils.clh-91- *
##############################################
gromacs-2021~beta2/src/gromacs/gpu_utils/device_utils.clh-111-
gromacs-2021~beta2/src/gromacs/gpu_utils/device_utils.clh:112:/* \brief Atomically increment the float3 value at address addr (in local memory) with value val.
gromacs-2021~beta2/src/gromacs/gpu_utils/device_utils.clh-113- *
##############################################
gromacs-2021~beta2/src/gromacs/timing/cyclecounter.h-91-#elif ((defined(__hppa__) || defined(__hppa)) && defined(__GNUC__))
gromacs-2021~beta2/src/gromacs/timing/cyclecounter.h:92:/* HP PA-RISC, inline asm with gcc */
gromacs-2021~beta2/src/gromacs/timing/cyclecounter.h-93-typedef unsigned long gmx_cycles_t;
##############################################
gromacs-2021~beta2/src/gromacs/timing/cyclecounter.h-206- unsigned int cycles_lo, cycles_hi;
gromacs-2021~beta2/src/gromacs/timing/cyclecounter.h:207: asm volatile("mrrc p15, 1, %0, %1, c14" : "=r"(cycles_lo), "=r"(cycles_hi));
gromacs-2021~beta2/src/gromacs/timing/cyclecounter.h-208- return ((gmx_cycles_t)cycles_lo) | (((gmx_cycles_t)cycles_hi) << 32);
##############################################
gromacs-2021~beta2/src/gromacs/timing/cyclecounter.h-250-{
gromacs-2021~beta2/src/gromacs/timing/cyclecounter.h:251: /* HP PA-RISC, inline asm with gcc */
gromacs-2021~beta2/src/gromacs/timing/cyclecounter.h-252- gmx_cycles_t ret;
##############################################
gromacs-2021~beta2/src/gromacs/timing/cyclecounter.h-461-{
gromacs-2021~beta2/src/gromacs/timing/cyclecounter.h:462: /* HP PA-RISC, inline asm with gcc */
gromacs-2021~beta2/src/gromacs/timing/cyclecounter.h-463- return 1;
##############################################
gromacs-2021~beta2/src/gromacs/commandline/cmdlineprogramcontext.cpp-335- fullBinaryPath_ = Path::normalize(Path::resolveSymlinks(fullBinaryPath_));
gromacs-2021~beta2/src/gromacs/commandline/cmdlineprogramcontext.cpp:336: // TODO: Investigate/Consider using a dladdr()-based solution.
gromacs-2021~beta2/src/gromacs/commandline/cmdlineprogramcontext.cpp-337- // Potentially less portable, but significantly simpler, and also works
##############################################
gromacs-2021~beta2/src/gromacs/hardware/identifyavx512fmaunits.cpp-68-
gromacs-2021~beta2/src/gromacs/hardware/identifyavx512fmaunits.cpp:69:#if GMX_X86_GCC_INLINE_ASM && SIMD_AVX_512_CXX_SUPPORTED
gromacs-2021~beta2/src/gromacs/hardware/identifyavx512fmaunits.cpp-70-/*\ brief Loop over mixed FMA and shuffle AVX512 instructions
##############################################
gromacs-2021~beta2/src/gromacs/hardware/identifyavx512fmaunits.cpp-83- uint64_t cycles;
gromacs-2021~beta2/src/gromacs/hardware/identifyavx512fmaunits.cpp:84: // Unfortunately we need to resort to inline ASM since we are
gromacs-2021~beta2/src/gromacs/hardware/identifyavx512fmaunits.cpp-85- // making a choice based on timing, and without efficient optimization
##############################################
gromacs-2021~beta2/src/gromacs/hardware/identifyavx512fmaunits.cpp-175- uint64_t cycles;
gromacs-2021~beta2/src/gromacs/hardware/identifyavx512fmaunits.cpp:176: // Unfortunately we need to resort to inline ASM since we are
gromacs-2021~beta2/src/gromacs/hardware/identifyavx512fmaunits.cpp-177- // making a choice based on timing, and without efficient optimization
##############################################
gromacs-2021~beta2/src/gromacs/hardware/identifyavx512fmaunits.cpp-246-
gromacs-2021~beta2/src/gromacs/hardware/identifyavx512fmaunits.cpp:247:#endif // GMX_X86_GCC_INLINE_ASM && SIMD_AVX_512_CXX_SUPPORTED
gromacs-2021~beta2/src/gromacs/hardware/identifyavx512fmaunits.cpp-248-
##############################################
gromacs-2021~beta2/src/gromacs/hardware/identifyavx512fmaunits.cpp-280- {
gromacs-2021~beta2/src/gromacs/hardware/identifyavx512fmaunits.cpp:281:#if GMX_X86_GCC_INLINE_ASM && SIMD_AVX_512_CXX_SUPPORTED
gromacs-2021~beta2/src/gromacs/hardware/identifyavx512fmaunits.cpp-282- result = checkDualAvx512FmaUnits() ? 2 : 1;
##############################################
gromacs-2021~beta2/src/gromacs/hardware/cpuinfo.cpp-47- * macro GMX_CPUINFO_STANDALONE is defined. In this case you likely also need to
gromacs-2021~beta2/src/gromacs/hardware/cpuinfo.cpp:48: * define GMX_X86_GCC_INLINE_ASM if you are on x86; without inline assembly
gromacs-2021~beta2/src/gromacs/hardware/cpuinfo.cpp-49- * support it is not possible to perform the actual detection on Linux/Mac.
##############################################
gromacs-2021~beta2/src/gromacs/hardware/cpuinfo.cpp-207-
gromacs-2021~beta2/src/gromacs/hardware/cpuinfo.cpp:208:#endif // check for inline asm on x86
gromacs-2021~beta2/src/gromacs/hardware/cpuinfo.cpp-209- }
##############################################
gromacs-2021~beta2/src/gromacs/gromacs-config.cmake.cmakein-56-endif()
gromacs-2021~beta2/src/gromacs/gromacs-config.cmake.cmakein:57:include(${_gmx_import_file})
gromacs-2021~beta2/src/gromacs/gromacs-config.cmake.cmakein-58-unset(_gmx_import_file)
##############################################
gromacs-2021~beta2/src/gromacs/utility/coolstuff.cpp-906- { "I'm no model lady. A model's just an imitation of the real thing.", "Mae West" },
gromacs-2021~beta2/src/gromacs/utility/coolstuff.cpp:907: { "Science is the great antidote to the poison of enthusiasm and superstition.",
gromacs-2021~beta2/src/gromacs/utility/coolstuff.cpp-908- "Adam Smith, Wealth of Nations, 1776" },
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gromacs-2021~beta2/src/gromacs/utility/coolstuff.cpp-1567- { "The message here is that Thermodynamic Integration sucks.", "Berk Hess" },
gromacs-2021~beta2/src/gromacs/utility/coolstuff.cpp:1568: { "Enthusiasm is the mother of effort, and without it nothing great was ever achieved.",
gromacs-2021~beta2/src/gromacs/utility/coolstuff.cpp-1569- "Ralph Waldo Emerson" },
##############################################
gromacs-2021~beta2/docs/CMakeLists.txt-523- if (EXISTS ${RELENG_PATH}/docs/FileList.cmake)
gromacs-2021~beta2/docs/CMakeLists.txt:524: include(${RELENG_PATH}/docs/FileList.cmake)
gromacs-2021~beta2/docs/CMakeLists.txt-525- gmx_add_sphinx_source_files(
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gromacs-2021~beta2/docs/dev-manual/gitlab.rst-221- use specific versions of CMake, please write the job *script* sections
gromacs-2021~beta2/docs/dev-manual/gitlab.rst:222: using ``$CMAKE`` instead of ``cmake`` and begin the *script* section with
gromacs-2021~beta2/docs/dev-manual/gitlab.rst:223: a line such as ``- CMAKE=${CMAKE:-$(which cmake)}``. Specify a CMake
gromacs-2021~beta2/docs/dev-manual/gitlab.rst-224- version by setting the *CMAKE* variable to the full executable path for
##############################################
gromacs-2021~beta2/docs/dev-manual/build-system.rst-367- ``clang-tidy -fix-errors -header-filter '.*' {file}``, to fix all files in parallel
gromacs-2021~beta2/docs/dev-manual/build-system.rst:368: ``run-clang-tidy.py -fix -header-filter '.*' '(?<!/selection/parser\.cpp|selection/scanner\.cpp)$'``,
gromacs-2021~beta2/docs/dev-manual/build-system.rst:369: and to fix all modified files ``run-clang-tidy.py -fix -header-filter '.*' $(git diff HEAD --name-only)``.
gromacs-2021~beta2/docs/dev-manual/build-system.rst-370- The run-clang-tidy.py script is in the
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gromacs-2021~beta2/docs/dev-manual/containers.rst-45-For more granularity,
gromacs-2021~beta2/docs/dev-manual/containers.rst:46:consider equivalent expressions ``${CI_REGISTRY}/${CI_PROJECT_PATH}``
gromacs-2021~beta2/docs/dev-manual/containers.rst:47:or ``${CI_REGISTRY}/${CI_PROJECT_NAMESPACE}/${CI_PROJECT_NAME}``
gromacs-2021~beta2/docs/dev-manual/containers.rst-48-Ref: https://docs.gitlab.com/ee/ci/variables/predefined_variables.html
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gromacs-2021~beta2/docs/dev-manual/contribute.rst-76- spans, and a proposed change affecting 10,000 lines of code is
gromacs-2021~beta2/docs/dev-manual/contribute.rst:77: likely to generate little enthusiasm from other developers to review
gromacs-2021~beta2/docs/dev-manual/contribute.rst-78- it. Your local git commit history is likely full of changes that are
##############################################
gromacs-2021~beta2/docs/gmxapi/userguide/install.rst-397-
gromacs-2021~beta2/docs/gmxapi/userguide/install.rst:398:In the following example, ``${SUFFIX}`` is the suffix that distinguishes the
gromacs-2021~beta2/docs/gmxapi/userguide/install.rst-399-particular build of GROMACS you want to target (refer to GROMACS installation
gromacs-2021~beta2/docs/gmxapi/userguide/install.rst:400:instructions for more information.) ``${SUFFIX}`` may simply be empty, or ``''``.
gromacs-2021~beta2/docs/gmxapi/userguide/install.rst-401-
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gromacs-2021~beta2/docs/install-guide/index.rst-1017-files will be installed at
gromacs-2021~beta2/docs/install-guide/index.rst:1018:``/your/installation/prefix/here/share/cmake/gromacs${GMX_LIBS_SUFFIX}/gromacs-toolchain${GMX_LIBS_SUFFIX}.cmake``
gromacs-2021~beta2/docs/install-guide/index.rst:1019:where ``${GMX_LIBS_SUFFIX}`` is :ref:`as documented above <suffixes>`.
gromacs-2021~beta2/docs/install-guide/index.rst-1020-
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gromacs-2021~beta2/docs/reference-manual/file-formats.rst-1044-To use the library function include ``"gromacs/fileio/xtcio.h"``
gromacs-2021~beta2/docs/reference-manual/file-formats.rst:1045:in your file and link with ``-lgmx.$(CPU)``.
gromacs-2021~beta2/docs/reference-manual/file-formats.rst-1046-
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gromacs-2021~beta2/docs/reference-manual/file-formats.rst-1075-
gromacs-2021~beta2/docs/reference-manual/file-formats.rst:1076:To link your program use ``-L$(GMXHOME)/lib/$(CPU) -lxtcf``
gromacs-2021~beta2/docs/reference-manual/file-formats.rst-1077-on your linker command line.
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gromacs-2021~beta2/docs/reference-manual/topologies/force-field-organization.rst-12-the presence of ``<name>.ff`` directories in the
gromacs-2021~beta2/docs/reference-manual/topologies/force-field-organization.rst:13:``$GMXLIB/share/gromacs/top`` sub-directory and/or the
gromacs-2021~beta2/docs/reference-manual/topologies/force-field-organization.rst-14-working directory. The information regarding the location of the force
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gromacs-2021~beta2/docs/how-to/special.rst-37-* Set the ``-radius`` option in :ref:`gmx solvate` to change the water exclusion radius,
gromacs-2021~beta2/docs/how-to/special.rst:38:* copy ``vdwradii.dat`` from your ``$GMXLIB`` location to the working directory, and edit it to
gromacs-2021~beta2/docs/how-to/special.rst-39- increase the radii of your lipid atoms (between 0.35 and 0.5nm is suggested for carbon) to
##############################################
gromacs-2021~beta2/docs/user-guide/environment-variables.rst-2-.. no longer present in the code.
gromacs-2021~beta2/docs/user-guide/environment-variables.rst:3:.. ( export INPUT_FILE='docs/user-guide/environment-variables.rst' GIT_PAGER="cat "; for s in $(grep '^`' $INPUT_FILE | sed 's/`//g' | sed 's/,/ /g'); do count=$(git grep $s | grep -v $INPUT_FILE | wc -l); [ $count -eq 0 ] && printf "%-30s%s\n" $s $count; done ; )
gromacs-2021~beta2/docs/user-guide/environment-variables.rst-4-.. Another useful one-liner to find undocumentedvariables:
gromacs-2021~beta2/docs/user-guide/environment-variables.rst:5:.. ( export INPUT_FILE=docs/user-guide/environment-variables.rst; GIT_PAGER="cat "; for ss in `for s in $(git grep getenv | sed 's/.*getenv("\(.*\)".*/\1/' | sort -u | grep '^[A-Z]'); do [ $(grep $s $INPUT_FILE -c) -eq 0 ] && echo $s; done `; do git grep $ss ; done )
gromacs-2021~beta2/docs/user-guide/environment-variables.rst-6-
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gromacs-2021~beta2/docs/user-guide/faq.rst-36- Suitable equilibrated boxes of solvent :ref:`structure files <gmx-structure-files>` can be found
gromacs-2021~beta2/docs/user-guide/faq.rst:37: in the ``$GMXDIR/share/gromacs/top`` directory. That location will be searched by default
gromacs-2021~beta2/docs/user-guide/faq.rst-38- by :ref:`solvate <gmx solvate>`, for example by using ``-cs spc216.gro`` as an argument.
##############################################
gromacs-2021~beta2/docs/user-guide/faq.rst-42- :ref:`grompp <gmx grompp>`. These are available for some force fields, and may be
gromacs-2021~beta2/docs/user-guide/faq.rst:43: found in the respective subfolder of ``$GMXDIR/share/gromacs/top``.
gromacs-2021~beta2/docs/user-guide/faq.rst-44-
##############################################
gromacs-2021~beta2/docs/user-guide/faq.rst-50- You can either remove those waters by hand (and do the accounting for molecule types in the
gromacs-2021~beta2/docs/user-guide/faq.rst:51: :ref:`topology <top>` file), or set up a local copy of the ``vdwradii.dat`` file from the ``$GMXLIB``
gromacs-2021~beta2/docs/user-guide/faq.rst-52- directory, specific for your project and located in your working directory. In it, you can
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gromacs-2021~beta2/tests/physicalvalidation/physical_validation/util/kinetic_energy.py-291- # an easy one), but by far not the last. So let's just resort to non-parallel
gromacs-2021~beta2/tests/physicalvalidation/physical_validation/util/kinetic_energy.py:292: # execution:
gromacs-2021~beta2/tests/physicalvalidation/physical_validation/util/kinetic_energy.py-293- kin_molec = [calc_molec_kinetic_energy(r, v, masses, molec_idx, natoms, nmolecs)
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gromacs-2021~beta2/api/gmxapi/cpp/cmake/gmxapi-config.cmake.in-4-# https://cmake.org/cmake/help/v3.4/module/CMakePackageConfigHelpers.html#command:configure_package_config_file
gromacs-2021~beta2/api/gmxapi/cpp/cmake/gmxapi-config.cmake.in:5:include("${CMAKE_CURRENT_LIST_DIR}/gmxapi.cmake")
gromacs-2021~beta2/api/gmxapi/cpp/cmake/gmxapi-config.cmake.in-6-check_required_components(gmxapi)
##############################################
gromacs-2021~beta2/api/nblib/CMakeLists.txt-81- endif()
gromacs-2021~beta2/api/nblib/CMakeLists.txt:82: include(${TESTUTILS_DIR}/TestMacros.cmake)
gromacs-2021~beta2/api/nblib/CMakeLists.txt-83-endif()
##############################################
gromacs-2021~beta2/cmake/gmxManageTNG.cmake-81- endif()
gromacs-2021~beta2/cmake/gmxManageTNG.cmake:82: include(${BUNDLED_TNG_LOCATION}/BuildTNG.cmake)
gromacs-2021~beta2/cmake/gmxManageTNG.cmake-83- add_tng_io_library(tng_io OBJECT ${_zlib_arg})
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gromacs-2021~beta2/cmake/gmxTestInlineASM.cmake-35-
gromacs-2021~beta2/cmake/gmxTestInlineASM.cmake:36:# - Define macro to check GCC x86 inline ASM support
gromacs-2021~beta2/cmake/gmxTestInlineASM.cmake-37-#
##############################################
gromacs-2021~beta2/cmake/gmxTestInlineASM.cmake-39-#
gromacs-2021~beta2/cmake/gmxTestInlineASM.cmake:40:# VARIABLE will be set to true if GCC x86 inline asm works.
gromacs-2021~beta2/cmake/gmxTestInlineASM.cmake-41-
##############################################
gromacs-2021~beta2/cmake/gmxTestInlineASM.cmake-51- if(${VARIABLE})
gromacs-2021~beta2/cmake/gmxTestInlineASM.cmake:52: MESSAGE(STATUS "Checking for GCC x86 inline asm - supported")
gromacs-2021~beta2/cmake/gmxTestInlineASM.cmake-53- set(${VARIABLE} 1 CACHE INTERNAL "Result of test for GCC x86 inline asm" FORCE)
gromacs-2021~beta2/cmake/gmxTestInlineASM.cmake-54- else()
gromacs-2021~beta2/cmake/gmxTestInlineASM.cmake:55: MESSAGE(STATUS "Checking for GCC x86 inline asm - not supported")
gromacs-2021~beta2/cmake/gmxTestInlineASM.cmake-56- set(${VARIABLE} 0 CACHE INTERNAL "Result of test for GCC x86 inline asm" FORCE)
##############################################
gromacs-2021~beta2/cmake/gmxManageLinearAlgebraLibraries.cmake-134- GMX_${name}_USER
gromacs-2021~beta2/cmake/gmxManageLinearAlgebraLibraries.cmake:135: "Use a ${name} library found on the system (OFF), or a ${name} library supplied by the user (any other value, which is a full path to that ${name} library)"
gromacs-2021~beta2/cmake/gmxManageLinearAlgebraLibraries.cmake-136- FILEPATH "" GMX_EXTERNAL_${name})
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gromacs-2021~beta2/cmake/gmxConfigureVersionInfo.cmake-34-
gromacs-2021~beta2/cmake/gmxConfigureVersionInfo.cmake:35:include(${VERSION_VARIABLES})
gromacs-2021~beta2/cmake/gmxConfigureVersionInfo.cmake-36-configure_file(${VERSION_CMAKEIN} ${VERSION_OUT} @ONLY)
##############################################
gromacs-2021~beta2/cmake/with_asan_opts.sh-50-# Suppressions are not currently necessary, but can be introduced like this.
gromacs-2021~beta2/cmake/with_asan_opts.sh:51:#path=`dirname $0`
gromacs-2021~beta2/cmake/with_asan_opts.sh-52-#export LSAN_OPTIONS="suppressions=$path/../admin/lsan-suppressions.txt"
##############################################
gromacs-2021~beta2/cmake/TestInlineASM_gcc_x86.cpp-6-
gromacs-2021~beta2/cmake/TestInlineASM_gcc_x86.cpp:7: /* Test gcc inline asm for x86. Note that we CANNOT plainly use __x86_64__
gromacs-2021~beta2/cmake/TestInlineASM_gcc_x86.cpp-8- * to correspond to a 64-bit environment without also checking that __ILP32__
##############################################
gromacs-2021~beta2/cmake/gmxDetectSimd.cmake-51-
gromacs-2021~beta2/cmake/gmxDetectSimd.cmake:52:# we rely on inline asm support for GNU!
gromacs-2021~beta2/cmake/gmxDetectSimd.cmake-53-include(gmxTestInlineASM)
##############################################
gromacs-2021~beta2/scripts/GMXRC.csh.cmakein-17-set tmppath = ""
gromacs-2021~beta2/scripts/GMXRC.csh.cmakein:18:foreach i ( `echo $@LD_LIBRARY_PATH@ | sed "s/:/ /g"` )
gromacs-2021~beta2/scripts/GMXRC.csh.cmakein-19- if ( "$i" != "$GMXLDLIB" ) then
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gromacs-2021~beta2/scripts/GMXRC.csh.cmakein-30-set tmppath = ""
gromacs-2021~beta2/scripts/GMXRC.csh.cmakein:31:foreach i ( `echo $PKG_CONFIG_PATH | sed "s/:/ /g"` )
gromacs-2021~beta2/scripts/GMXRC.csh.cmakein-32- if ( "$i" != "$GMXLDLIB/pkgconfig" ) then
##############################################
gromacs-2021~beta2/scripts/GMXRC.csh.cmakein-43-set tmppath = ""
gromacs-2021~beta2/scripts/GMXRC.csh.cmakein:44:foreach i ( `echo $PATH | sed "s/:/ /g"` )
gromacs-2021~beta2/scripts/GMXRC.csh.cmakein-45- if ( "$i" != "$GMXBIN" ) then
##############################################
gromacs-2021~beta2/scripts/GMXRC.csh.cmakein-56-set tmppath = ""
gromacs-2021~beta2/scripts/GMXRC.csh.cmakein:57:foreach i ( `echo $MANPATH | sed "s/:/ /g"` )
gromacs-2021~beta2/scripts/GMXRC.csh.cmakein-58- if ( "$i" != "$GMXMAN" ) then
##############################################
gromacs-2021~beta2/admin/clang-tidy.sh-174-if [[ $tidy_mode != "off" && -s $tmpdir/filelist_clangtidy ]] ; then
gromacs-2021~beta2/admin/clang-tidy.sh:175: $RUN_CLANG_TIDY `cat $tmpdir/filelist_clangtidy` -header-filter=.* -j $concurrency -fix -quiet -extra-arg=--cuda-host-only -extra-arg=-nocudainc>$tmpdir/clang-tidy.out 2>&1
gromacs-2021~beta2/admin/clang-tidy.sh-176- awk '/warning/,/clang-tidy|^$/' $tmpdir/clang-tidy.out | grep -v "warnings generated." | grep -v "Suppressed .* warnings" | grep -v "clang-analyzer" | grep -v "to display errors from all non" | sed '/^\s*$/d' > $tmpdir/clang-tidy-warnings.out
##############################################
gromacs-2021~beta2/admin/clang-format.sh-159-if [[ $format_mode != "off" && -s $tmpdir/filelist_clangformat ]] ; then
gromacs-2021~beta2/admin/clang-format.sh:160: $CLANG_FORMAT -i `cat $tmpdir/filelist_clangformat` >$tmpdir/clang-format.out 2>&1
gromacs-2021~beta2/admin/clang-format.sh-161- if [ -s $tmpdir/clang-format.out ]; then
##############################################
gromacs-2021~beta2/python_packaging/src/setup.py-67-
gromacs-2021~beta2/python_packaging/src/setup.py:68:If you have multiple builds of GROMACS, distinguished by a suffix `$SUFFIX`, the
gromacs-2021~beta2/python_packaging/src/setup.py-69-tool chain directory will use that suffix.
##############################################
gromacs-2021~beta2/python_packaging/src/external/pybind/tools/pybind11Config.cmake.in-83-if(NOT TARGET ${PN}::pybind11)
gromacs-2021~beta2/python_packaging/src/external/pybind/tools/pybind11Config.cmake.in:84: include("${CMAKE_CURRENT_LIST_DIR}/${PN}Targets.cmake")
gromacs-2021~beta2/python_packaging/src/external/pybind/tools/pybind11Config.cmake.in-85-
##############################################
gromacs-2021~beta2/python_packaging/test/README.md-31-
gromacs-2021~beta2/python_packaging/test/README.md:32:`pytest $LOCAL_REPO_DIR/python_packaging/test`
gromacs-2021~beta2/python_packaging/test/README.md-33-
gromacs-2021~beta2/python_packaging/test/README.md:34:where `$LOCAL_REPO_DIR` is the path to the local copy of the GROMACS source repository.
gromacs-2021~beta2/python_packaging/test/README.md-35-
##############################################
gromacs-2021~beta2/python_packaging/test/README.md-37-
gromacs-2021~beta2/python_packaging/test/README.md:38:`mpiexec -n 2 python -m mpi4py -m pytest $LOCAL_REPO_DIR/python_packaging/test`
gromacs-2021~beta2/python_packaging/test/README.md-39-
##############################################
gromacs-2021~beta2/python_packaging/sample_restraint/.travis.yml-53- # get exactly one Python version: the last listed patch version for the selected minor version
gromacs-2021~beta2/python_packaging/sample_restraint/.travis.yml:54: - pyenv whence python${PY} && export PY_VER=`pyenv whence python${PY} | tail -1`
gromacs-2021~beta2/python_packaging/sample_restraint/.travis.yml-55- - pyenv shell $PY_VER && pyenv shell
gromacs-2021~beta2/python_packaging/sample_restraint/.travis.yml-56-# - python-config --includes
gromacs-2021~beta2/python_packaging/sample_restraint/.travis.yml:57: - pyenv prefix ${PY_VER} && export PYTHON_PREFIX=`pyenv prefix ${PY_VER}`
gromacs-2021~beta2/python_packaging/sample_restraint/.travis.yml-58- - pyenv which python && export PYTHON=`pyenv which python`
##############################################
gromacs-2021~beta2/python_packaging/docker/README.md-35- # Use DOCKER_CORES to let `make` use all cores available to the Docker engine.
gromacs-2021~beta2/python_packaging/docker/README.md:36: # optionally include an additional `--build-arg REF=${FORKPOINT}`
gromacs-2021~beta2/python_packaging/docker/README.md-37- docker build -t gmxapi/gromacs-mpich --build-arg DOCKER_CORES=4 -f gromacs.dockerfile ../..
##############################################
gromacs-2021~beta2/debian/changelog-959- - 40_hppa_asm.dpatch: Attempt to correct FTBFS on HPPA
gromacs-2021~beta2/debian/changelog:960: inline ASM code by replacing an undefined variable.
gromacs-2021~beta2/debian/changelog-961- (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=260)